-------------------------------------
Thu Jan 16 09:36:10 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

BLM has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  BLM ( 1  of  38 )
CAF1B has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CAF1B ( 2  of  38 )
CHD4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CHD4 ( 3  of  38 )
DEK has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  DEK ( 4  of  38 )
FEN1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  FEN1 ( 5  of  38 )
H2AX has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  H2AX ( 6  of  38 )
HCFC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
HDAC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
MBD3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MBD3 ( 9  of  38 )
MDC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MDC1 ( 10  of  38 )
MED4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MED4 ( 11  of  38 )
MRE11 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MRE11 ( 12  of  38 )
MSH2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MSH2 ( 13  of  38 )
MTA2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MTA2 ( 14  of  38 )
NBN has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NBN ( 15  of  38 )
NUCL has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NUCL ( 16  of  38 )
P53 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  P53 ( 17  of  38 )
PARP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PARP1 ( 18  of  38 )
PCNA has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PCNA ( 19  of  38 )
POLD1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLD1 ( 20  of  38 )
POLR2E has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLR2E ( 21  of  38 )
PRKDC has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PRKDC ( 22  of  38 )
RALY has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RALY ( 23  of  38 )
RBBP4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RBBP4 ( 24  of  38 )
RPA1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RPA1 ( 25  of  38 )
SKIV2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
SPT16H has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SPT16H ( 27  of  38 )
SSRP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SSRP1 ( 28  of  38 )
SUMO1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
TFDP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TFDP1 ( 31  of  38 )
TOP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TOP1 ( 32  of  38 )
TRIM28 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
WRNIP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
XRCC3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
XRCC5 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
XRCC6 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC6 ( 37  of  38 )
YBOX1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  YBOX1 ( 38  of  38 )
-------------------------------------
Thu Jan 16 09:38:42 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

BLM has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  BLM ( 1  of  38 )
CAF1B has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CAF1B ( 2  of  38 )
CHD4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CHD4 ( 3  of  38 )
DEK has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  DEK ( 4  of  38 )
FEN1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  FEN1 ( 5  of  38 )
H2AX has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  H2AX ( 6  of  38 )
HCFC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
HDAC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
MBD3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MBD3 ( 9  of  38 )
MDC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MDC1 ( 10  of  38 )
MED4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MED4 ( 11  of  38 )
MRE11 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MRE11 ( 12  of  38 )
MSH2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MSH2 ( 13  of  38 )
MTA2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MTA2 ( 14  of  38 )
NBN has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NBN ( 15  of  38 )
NUCL has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NUCL ( 16  of  38 )
P53 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  P53 ( 17  of  38 )
PARP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PARP1 ( 18  of  38 )
PCNA has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PCNA ( 19  of  38 )
POLD1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLD1 ( 20  of  38 )
POLR2E has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLR2E ( 21  of  38 )
PRKDC has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PRKDC ( 22  of  38 )
RALY has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RALY ( 23  of  38 )
RBBP4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RBBP4 ( 24  of  38 )
RPA1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RPA1 ( 25  of  38 )
SKIV2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
SPT16H has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SPT16H ( 27  of  38 )
SSRP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SSRP1 ( 28  of  38 )
SUMO1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
TFDP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TFDP1 ( 31  of  38 )
TOP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TOP1 ( 32  of  38 )
TRIM28 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
WRNIP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
XRCC3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
XRCC5 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
XRCC6 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC6 ( 37  of  38 )
YBOX1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  YBOX1 ( 38  of  38 )
-------------------------------------
Thu Jan 16 09:45:02 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

BLM has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  BLM ( 1  of  38 )
CAF1B has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CAF1B ( 2  of  38 )
CHD4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CHD4 ( 3  of  38 )
DEK has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  DEK ( 4  of  38 )
FEN1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  FEN1 ( 5  of  38 )
H2AX has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  H2AX ( 6  of  38 )
HCFC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
HDAC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
MBD3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MBD3 ( 9  of  38 )
MDC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MDC1 ( 10  of  38 )
MED4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MED4 ( 11  of  38 )
MRE11 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MRE11 ( 12  of  38 )
MSH2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MSH2 ( 13  of  38 )
MTA2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MTA2 ( 14  of  38 )
NBN has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NBN ( 15  of  38 )
NUCL has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NUCL ( 16  of  38 )
P53 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  P53 ( 17  of  38 )
PARP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PARP1 ( 18  of  38 )
PCNA has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PCNA ( 19  of  38 )
POLD1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLD1 ( 20  of  38 )
POLR2E has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLR2E ( 21  of  38 )
PRKDC has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PRKDC ( 22  of  38 )
RALY has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RALY ( 23  of  38 )
RBBP4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RBBP4 ( 24  of  38 )
RPA1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RPA1 ( 25  of  38 )
SKIV2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
SPT16H has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SPT16H ( 27  of  38 )
SSRP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SSRP1 ( 28  of  38 )
SUMO1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
TFDP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TFDP1 ( 31  of  38 )
TOP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TOP1 ( 32  of  38 )
TRIM28 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
WRNIP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
XRCC3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
XRCC5 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
XRCC6 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC6 ( 37  of  38 )
YBOX1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There are 333 features (AIVEFLSNLAR_2_y4_1, AIVEFLSNLAR_2_y5_1, AIVEFLSNLAR_2_y6_1, AIVEFLSNLAR_2_y7_1, AIVEFLSNLAR_2_y8_1, AIVEFLSNLAR_2_y9_1, VTLNTLQAWSK_2_y3_1, VTLNTLQAWSK_2_y4_1, VTLNTLQAWSK_2_y6_1, VTLNTLQAWSK_2_y8_1, LLEQALVIEEQLR_2_y4_1, LLEQALVIEEQLR_2_y5_1, LLEQALVIEEQLR_2_y6_1, LLEQALVIEEQLR_2_y7_1, LLEQALVIEEQLR_2_y8_1, LLEQALVIEEQLR_2_y9_1, TVQTAVFLYSLYK_2_y10_1, TVQTAVFLYSLYK_2_y11_1, TVQTAVFLYSLYK_2_y4_1, TVQTAVFLYSLYK_2_y5_1, TVQTAVFLYSLYK_2_y6_1, TVQTAVFLYSLYK_2_y7_1, TVQTAVFLYSLYK_2_y8_1, YYAVNYPLR_2_y3_1, YYAVNYPLR_2_y4_1, YYAVNYPLR_2_y5_1, YYAVNYPLR_2_y6_1, YYAVNYPLR_2_y7_1, LSGLNAFDIAEELVK_2_y10_1, LSGLNAFDIAEELVK_2_y11_1, LSGLNAFDIAEELVK_2_y4_1, LSGLNAFDIAEELVK_2_y5_1, LSGLNAFDIAEELVK_2_y8_1, LSGLNAFDIAEELVK_2_y9_1, NPGVWLNTTQPLCK_2_y10_1, NPGVWLNTTQPLCK_2_y8_1, NPGVWLNTTQPLCK_2_y9_1, DISSSLNSLADSNAR_2_y10_1, DISSSLNSLADSNAR_2_y11_1, DISSSLNSLADSNAR_2_y5_1, DISSSLNSLADSNAR_2_y6_1, DISSSLNSLADSNAR_2_y7_1, DISSSLNSLADSNAR_2_y8_1, DISSSLNSLADSNAR_2_y9_1, EAAFDDAVEER_2_y5_1, EAAFDDAVEER_2_y6_1, EAAFDDAVEER_2_y7_1, EAAFDDAVEER_2_y8_1, EAAFDDAVEER_2_y9_1, GEFGGFGSVSGK_2_y10_1, GEFGGFGSVSGK_2_y6_1, GEFGGFGSVSGK_2_y7_1, GEFGGFGSVSGK_2_y8_1, GEFGGFGSVSGK_2_y9_1, INHEGEVNR_2_y5_1, INHEGEVNR_2_y6_1, INHEGEVNR_2_y7_1, TPSSDVLVFDYTK_2_y11_1, TPSSDVLVFDYTK_2_y4_1, TPSSDVLVFDYTK_2_y5_1, TPSSDVLVFDYTK_2_y6_1, TPSSDVLVFDYTK_2_y7_1, TPSSDVLVFDYTK_2_y8_1, TPSSDVLVFDYTK_2_y9_1, NEGNIFPNPEATFVK_2_y10_1, NEGNIFPNPEATFVK_2_y11_1, NEGNIFPNPEATFVK_2_y4_1, NEGNIFPNPEATFVK_2_y5_1, NEGNIFPNPEATFVK_2_y7_1, NEGNIFPNPEATFVK_2_y8_1, NEGNIFPNPEATFVK_2_y9_1, ADVIQATGDAICIFR_2_y10_1, ADVIQATGDAICIFR_2_y11_1, ADVIQATGDAICIFR_2_y5_1, ADVIQATGDAICIFR_2_y6_1, ADVIQATGDAICIFR_2_y7_1, ADVIQATGDAICIFR_2_y9_1, LLSALEDLEVLSR_2_y10_1, LLSALEDLEVLSR_2_y5_1, LLSALEDLEVLSR_2_y6_1, LLSALEDLEVLSR_2_y8_1, LLSALEDLEVLSR_2_y9_1, EEVTELLAR_2_y3_1, EEVTELLAR_2_y4_1, EEVTELLAR_2_y5_1, EEVTELLAR_2_y6_1, GYLVTQDELDQTLEEFK_2_y10_1, GYLVTQDELDQTLEEFK_2_y11_1, GYLVTQDELDQTLEEFK_2_y4_1, GYLVTQDELDQTLEEFK_2_y6_1, GYLVTQDELDQTLEEFK_2_y7_1, GYLVTQDELDQTLEEFK_2_y9_1, DPPLAAVTTAVQELLR_2_y5_1, DPPLAAVTTAVQELLR_2_y6_1, DPPLAAVTTAVQELLR_2_y7_1, DPPLAAVTTAVQELLR_2_y8_1, DPPLAAVTTAVQELLR_2_y9_1, TQGELFLLLDSR_2_y10_1, TQGELFLLLDSR_2_y4_1, TQGELFLLLDSR_2_y5_1, TQGELFLLLDSR_2_y7_1, VIGQDSSEIHFK_2_y10_1, VIGQDSSEIHFK_2_y3_1, VIGQDSSEIHFK_2_y4_1, VIGQDSSEIHFK_2_y6_1, VIGQDSSEIHFK_2_y7_1, VIGQDSSEIHFK_2_y8_1, QSQLQELILQQIAFK_2_y10_1, QSQLQELILQQIAFK_2_y5_1, QSQLQELILQQIAFK_2_y6_1, QSQLQELILQQIAFK_2_y7_1, QSQLQELILQQIAFK_2_y8_1, SVGDGETVEFDVVEGEK_2_y10_1, SVGDGETVEFDVVEGEK_2_y11_1, SVGDGETVEFDVVEGEK_2_y5_1, SVGDGETVEFDVVEGEK_2_y6_1, SVGDGETVEFDVVEGEK_2_y7_1, SVGDGETVEFDVVEGEK_2_y8_1, TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, SICEVLDLER_2_y3_1, SICEVLDLER_2_y5_1, SICEVLDLER_2_y6_1, SICEVLDLER_2_y7_1, SICEVLDLER_2_y8_1, VYENYPTYDLTER_2_y10_1, VYENYPTYDLTER_2_y3_1, VYENYPTYDLTER_2_y4_1, VYENYPTYDLTER_2_y5_1, VYENYPTYDLTER_2_y7_1, VYENYPTYDLTER_2_y9_1, EAHQLFLEPEVLDPESVELK_2_y12_1, EAHQLFLEPEVLDPESVELK_2_y3_1, EAHQLFLEPEVLDPESVELK_2_y4_1, EAHQLFLEPEVLDPESVELK_2_y5_1, EAHQLFLEPEVLDPESVELK_2_y7_1, EAHQLFLEPEVLDPESVELK_2_y8_1, LIADVAPSAIR_2_y5_1, LIADVAPSAIR_2_y6_1, LIADVAPSAIR_2_y7_1, LIADVAPSAIR_2_y8_1, LIADVAPSAIR_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_1, ISVATGALEAAQGSK_2_y11_1, ISVATGALEAAQGSK_2_y12_1, ISVATGALEAAQGSK_2_y5_1, ISVATGALEAAQGSK_2_y6_1, ISVATGALEAAQGSK_2_y8_1, ISVATGALEAAQGSK_2_y9_1, SPAFVQLAPLSSK_2_y10_1, SPAFVQLAPLSSK_2_y5_1, SPAFVQLAPLSSK_2_y6_1, SPAFVQLAPLSSK_2_y7_1, SPAFVQLAPLSSK_2_y8_1, SPAFVQLAPLSSK_2_y9_1, SPISVPGGSALISNLGK_2_y10_1, SPISVPGGSALISNLGK_2_y11_1, SPISVPGGSALISNLGK_2_y12_1, SPISVPGGSALISNLGK_2_y5_1, SPISVPGGSALISNLGK_2_y6_1, GPLTVEETPR_2_y4_1, GPLTVEETPR_2_y5_1, GPLTVEETPR_2_y6_1, GPLTVEETPR_2_y7_1, GPLTVEETPR_2_y8_1, ADTGLETSTR_2_y3_1, ADTGLETSTR_2_y4_1, ADTGLETSTR_2_y5_1, ADTGLETSTR_2_y6_1, ADTGLETSTR_2_y7_1, ADTGLETSTR_2_y8_1, LLLAVFVTPLTDLR_2_y10_1, LLLAVFVTPLTDLR_2_y11_1, LLLAVFVTPLTDLR_2_y6_1, LLLAVFVTPLTDLR_2_y8_1, LLLAVFVTPLTDLR_2_y9_1, NCAILIENDQSISR_2_y3_1, NCAILIENDQSISR_2_y4_1, NCAILIENDQSISR_2_y5_1, FGYVDFESAEDLEK_2_y10_1, FGYVDFESAEDLEK_2_y11_1, FGYVDFESAEDLEK_2_y7_1, FGYVDFESAEDLEK_2_y8_1, FGYVDFESAEDLEK_2_y9_1, GLSEDTTEETLK_2_y10_1, GLSEDTTEETLK_2_y4_1, GLSEDTTEETLK_2_y6_1, GLSEDTTEETLK_2_y7_1, GLSEDTTEETLK_2_y8_1, ALPNNTSSSPQPK_2_y10_1, ALPNNTSSSPQPK_2_y11_1, ALPNNTSSSPQPK_2_y6_1, ALPNNTSSSPQPK_2_y7_1, ALPNNTSSSPQPK_2_y8_1, ALPNNTSSSPQPK_2_y9_1, ELNEALELK_2_y4_1, ELNEALELK_2_y5_1, ELNEALELK_2_y6_1, ELNEALELK_2_y7_1, SVTCTYSPALNK_2_y10_1, SVTCTYSPALNK_2_y3_1, SVTCTYSPALNK_2_y5_1, SVTCTYSPALNK_2_y7_1, SVTCTYSPALNK_2_y8_1, SVTCTYSPALNK_2_y9_1, SLQELFLAHILSPWGAEVK_2_y10_1, SLQELFLAHILSPWGAEVK_2_y12_1, SLQELFLAHILSPWGAEVK_2_y7_1, SLQELFLAHILSPWGAEVK_2_y8_1, SLQELFLAHILSPWGAEVK_2_y9_1, AEDNADTLALVFEAPNQEK_2_y10_1, AEDNADTLALVFEAPNQEK_2_y11_1, AEDNADTLALVFEAPNQEK_2_y5_1, AEDNADTLALVFEAPNQEK_2_y6_1, AEDNADTLALVFEAPNQEK_2_y7_1, AEDNADTLALVFEAPNQEK_2_y8_1, AEDNADTLALVFEAPNQEK_2_y9_1, DLSHIGDAVVISCAK_2_y10_1, DLSHIGDAVVISCAK_2_y11_1, DLSHIGDAVVISCAK_2_y4_1, DLSHIGDAVVISCAK_2_y5_1, DLSHIGDAVVISCAK_2_y6_1, DLSHIGDAVVISCAK_2_y7_1, DLSHIGDAVVISCAK_2_y8_1, DLSHIGDAVVISCAK_2_y9_1, LGLTEDQFIR_2_y3_1, LGLTEDQFIR_2_y4_1, LGLTEDQFIR_2_y5_1, LGLTEDQFIR_2_y6_1, LGLTEDQFIR_2_y7_1, ATQQQHDFTLTQTADGR_2_y10_1, ATQQQHDFTLTQTADGR_2_y11_1, ATQQQHDFTLTQTADGR_2_y12_1, ATQQQHDFTLTQTADGR_2_y7_1, TVGALQVLGTEAQSSLLK_2_y10_1, TVGALQVLGTEAQSSLLK_2_y11_1, TVGALQVLGTEAQSSLLK_2_y12_1, TVGALQVLGTEAQSSLLK_2_y13_1, TVGALQVLGTEAQSSLLK_2_y7_1, TVGALQVLGTEAQSSLLK_2_y9_1, STAVTTSSAK_2_y2_1, STAVTTSSAK_2_y3_1, STAVTTSSAK_2_y4_1, STAVTTSSAK_2_y5_1, STAVTTSSAK_2_y7_1, GWFDAEGQALDGVSISDLK_2_y10_1, GWFDAEGQALDGVSISDLK_2_y11_1, GWFDAEGQALDGVSISDLK_2_y13_1, GWFDAEGQALDGVSISDLK_2_y6_1, GWFDAEGQALDGVSISDLK_2_y9_1, VIDQQNGLYR_2_y2_1, VIDQQNGLYR_2_y4_1, VIDQQNGLYR_2_y5_1, VIDQQNGLYR_2_y6_1, VIDQQNGLYR_2_y7_1, VIDQQNGLYR_2_y8_1, VVPIASLTPYQSK_2_y11_1, VVPIASLTPYQSK_2_y5_1, VVPIASLTPYQSK_2_y6_1, VVPIASLTPYQSK_2_y8_1, VVPIASLTPYQSK_2_y9_1, AEEVATFFAK_2_y3_1, AEEVATFFAK_2_y4_1, AEEVATFFAK_2_y7_1, AEEVATFFAK_2_y8_1, ELTAPDENIPAK_2_y10_1, ELTAPDENIPAK_2_y6_1, ELTAPDENIPAK_2_y7_1, ELTAPDENIPAK_2_y9_1, GPVFAPPYEPLPENVK_2_y10_1, GPVFAPPYEPLPENVK_2_y11_1, GPVFAPPYEPLPENVK_2_y12_1, GPVFAPPYEPLPENVK_2_y5_1, GPVFAPPYEPLPENVK_2_y7_1, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_1, AGLNGLQLAVLAR_2_y4_1, AGLNGLQLAVLAR_2_y5_1, AGLNGLQLAVLAR_2_y6_1, AGLNGLQLAVLAR_2_y7_1, AGLNGLQLAVLAR_2_y8_1, AGLNGLQLAVLAR_2_y9_1, NHQGPLPPVPLHLR_2_y10_1, NHQGPLPPVPLHLR_2_y5_1, NHQGPLPPVPLHLR_2_y6_1, NHQGPLPPVPLHLR_2_y7_1, NHQGPLPPVPLHLR_2_y8_1, TILFIDEIHR_2_y5_1, TILFIDEIHR_2_y6_1, TILFIDEIHR_2_y7_1, TILFIDEIHR_2_y8_1, LVVIDSVAAPFR_2_y3_1, LVVIDSVAAPFR_2_y4_1, LVVIDSVAAPFR_2_y5_1, LVVIDSVAAPFR_2_y6_1, LVVIDSVAAPFR_2_y7_1, ANPQVGVAFPHIK_2_y4_1, ANPQVGVAFPHIK_2_y5_1, ANPQVGVAFPHIK_2_y6_1, ANPQVGVAFPHIK_2_y8_1, ANPQVGVAFPHIK_2_y9_1, SQLDIIIHSLK_2_y3_1, SQLDIIIHSLK_2_y4_1, SQLDIIIHSLK_2_y5_1, SQLDIIIHSLK_2_y6_1, SQLDIIIHSLK_2_y8_1, SQLDIIIHSLK_2_y9_1, ELVYPPDYNPEGK_2_y10_1, ELVYPPDYNPEGK_2_y4_1, ELVYPPDYNPEGK_2_y6_1, ELVYPPDYNPEGK_2_y8_1, SDSFENPVLQQHFR_2_y3_1, SDSFENPVLQQHFR_2_y4_1, SDSFENPVLQQHFR_2_y5_1, SDSFENPVLQQHFR_2_y6_1, SDSFENPVLQQHFR_2_y8_1, SDSFENPVLQQHFR_2_y9_1) that are missing intensities for an entire condition.  Intensities in these conditions have been imputed with the minimum intensity across all samples.
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
error : can't analyze CAF1B for comparison.
Testing a comparison for protein  CHD4 ( 3  of  38 )
error : can't analyze CHD4 for comparison.
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
error : can't analyze HCFC1 for comparison.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
error : can't analyze MBD3 for comparison.
Testing a comparison for protein  MDC1 ( 10  of  38 )
error : can't analyze MDC1 for comparison.
Testing a comparison for protein  MED4 ( 11  of  38 )
error : can't analyze MED4 for comparison.
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
error : can't analyze MSH2 for comparison.
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
error : can't analyze P53 for comparison.
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
error : can't analyze PCNA for comparison.
Testing a comparison for protein  POLD1 ( 20  of  38 )
error : can't analyze POLD1 for comparison.
Testing a comparison for protein  POLR2E ( 21  of  38 )
error : can't analyze POLR2E for comparison.
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
error : can't analyze RBBP4 for comparison.
Testing a comparison for protein  RPA1 ( 25  of  38 )
error : can't analyze RPA1 for comparison.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
error : can't analyze SKIV2 for comparison.
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
error : can't analyze TFDP1 for comparison.
Testing a comparison for protein  TOP1 ( 32  of  38 )
error : can't analyze TOP1 for comparison.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
error : can't analyze WRNIP1 for comparison.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
error : can't analyze XRCC3 for comparison.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 50 or more warnings (use warnings() to see the first 50)
The features that are missing intensities for an entire condition in Protein will be removed for fitting the model.
Testing a comparison for protein   ( 1  of  9 )
Protein BLM has only single transition, the simplied model is fitted
error : can't analyze BLM for comparison.
Error in `$<-.data.frame`(`*tmp*`, "residuals", value = NA) : 
  replacement has 1 row, data has 0
Calls: groupComparison -> $<- -> $<-.data.frame
Execution halted
-------------------------------------
Thu Jan 16 09:46:05 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

BLM has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  BLM ( 1  of  38 )
CAF1B has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CAF1B ( 2  of  38 )
CHD4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  CHD4 ( 3  of  38 )
DEK has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  DEK ( 4  of  38 )
FEN1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  FEN1 ( 5  of  38 )
H2AX has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  H2AX ( 6  of  38 )
HCFC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
HDAC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
MBD3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MBD3 ( 9  of  38 )
MDC1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MDC1 ( 10  of  38 )
MED4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MED4 ( 11  of  38 )
MRE11 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MRE11 ( 12  of  38 )
MSH2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MSH2 ( 13  of  38 )
MTA2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  MTA2 ( 14  of  38 )
NBN has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NBN ( 15  of  38 )
NUCL has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  NUCL ( 16  of  38 )
P53 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  P53 ( 17  of  38 )
PARP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PARP1 ( 18  of  38 )
PCNA has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PCNA ( 19  of  38 )
POLD1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLD1 ( 20  of  38 )
POLR2E has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  POLR2E ( 21  of  38 )
PRKDC has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  PRKDC ( 22  of  38 )
RALY has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RALY ( 23  of  38 )
RBBP4 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RBBP4 ( 24  of  38 )
RPA1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  RPA1 ( 25  of  38 )
SKIV2 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
SPT16H has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SPT16H ( 27  of  38 )
SSRP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SSRP1 ( 28  of  38 )
SUMO1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
TFDP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TFDP1 ( 31  of  38 )
TOP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TOP1 ( 32  of  38 )
TRIM28 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
WRNIP1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
XRCC3 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
XRCC5 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
XRCC6 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  XRCC6 ( 37  of  38 )
YBOX1 has some features that are missing intensities for an entire condition in Protein, The additive model (without interaction) will be fitted.
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There are 333 features (AIVEFLSNLAR_2_y4_1, AIVEFLSNLAR_2_y5_1, AIVEFLSNLAR_2_y6_1, AIVEFLSNLAR_2_y7_1, AIVEFLSNLAR_2_y8_1, AIVEFLSNLAR_2_y9_1, VTLNTLQAWSK_2_y3_1, VTLNTLQAWSK_2_y4_1, VTLNTLQAWSK_2_y6_1, VTLNTLQAWSK_2_y8_1, LLEQALVIEEQLR_2_y4_1, LLEQALVIEEQLR_2_y5_1, LLEQALVIEEQLR_2_y6_1, LLEQALVIEEQLR_2_y7_1, LLEQALVIEEQLR_2_y8_1, LLEQALVIEEQLR_2_y9_1, TVQTAVFLYSLYK_2_y10_1, TVQTAVFLYSLYK_2_y11_1, TVQTAVFLYSLYK_2_y4_1, TVQTAVFLYSLYK_2_y5_1, TVQTAVFLYSLYK_2_y6_1, TVQTAVFLYSLYK_2_y7_1, TVQTAVFLYSLYK_2_y8_1, YYAVNYPLR_2_y3_1, YYAVNYPLR_2_y4_1, YYAVNYPLR_2_y5_1, YYAVNYPLR_2_y6_1, YYAVNYPLR_2_y7_1, LSGLNAFDIAEELVK_2_y10_1, LSGLNAFDIAEELVK_2_y11_1, LSGLNAFDIAEELVK_2_y4_1, LSGLNAFDIAEELVK_2_y5_1, LSGLNAFDIAEELVK_2_y8_1, LSGLNAFDIAEELVK_2_y9_1, NPGVWLNTTQPLCK_2_y10_1, NPGVWLNTTQPLCK_2_y8_1, NPGVWLNTTQPLCK_2_y9_1, DISSSLNSLADSNAR_2_y10_1, DISSSLNSLADSNAR_2_y11_1, DISSSLNSLADSNAR_2_y5_1, DISSSLNSLADSNAR_2_y6_1, DISSSLNSLADSNAR_2_y7_1, DISSSLNSLADSNAR_2_y8_1, DISSSLNSLADSNAR_2_y9_1, EAAFDDAVEER_2_y5_1, EAAFDDAVEER_2_y6_1, EAAFDDAVEER_2_y7_1, EAAFDDAVEER_2_y8_1, EAAFDDAVEER_2_y9_1, GEFGGFGSVSGK_2_y10_1, GEFGGFGSVSGK_2_y6_1, GEFGGFGSVSGK_2_y7_1, GEFGGFGSVSGK_2_y8_1, GEFGGFGSVSGK_2_y9_1, INHEGEVNR_2_y5_1, INHEGEVNR_2_y6_1, INHEGEVNR_2_y7_1, TPSSDVLVFDYTK_2_y11_1, TPSSDVLVFDYTK_2_y4_1, TPSSDVLVFDYTK_2_y5_1, TPSSDVLVFDYTK_2_y6_1, TPSSDVLVFDYTK_2_y7_1, TPSSDVLVFDYTK_2_y8_1, TPSSDVLVFDYTK_2_y9_1, NEGNIFPNPEATFVK_2_y10_1, NEGNIFPNPEATFVK_2_y11_1, NEGNIFPNPEATFVK_2_y4_1, NEGNIFPNPEATFVK_2_y5_1, NEGNIFPNPEATFVK_2_y7_1, NEGNIFPNPEATFVK_2_y8_1, NEGNIFPNPEATFVK_2_y9_1, ADVIQATGDAICIFR_2_y10_1, ADVIQATGDAICIFR_2_y11_1, ADVIQATGDAICIFR_2_y5_1, ADVIQATGDAICIFR_2_y6_1, ADVIQATGDAICIFR_2_y7_1, ADVIQATGDAICIFR_2_y9_1, LLSALEDLEVLSR_2_y10_1, LLSALEDLEVLSR_2_y5_1, LLSALEDLEVLSR_2_y6_1, LLSALEDLEVLSR_2_y8_1, LLSALEDLEVLSR_2_y9_1, EEVTELLAR_2_y3_1, EEVTELLAR_2_y4_1, EEVTELLAR_2_y5_1, EEVTELLAR_2_y6_1, GYLVTQDELDQTLEEFK_2_y10_1, GYLVTQDELDQTLEEFK_2_y11_1, GYLVTQDELDQTLEEFK_2_y4_1, GYLVTQDELDQTLEEFK_2_y6_1, GYLVTQDELDQTLEEFK_2_y7_1, GYLVTQDELDQTLEEFK_2_y9_1, DPPLAAVTTAVQELLR_2_y5_1, DPPLAAVTTAVQELLR_2_y6_1, DPPLAAVTTAVQELLR_2_y7_1, DPPLAAVTTAVQELLR_2_y8_1, DPPLAAVTTAVQELLR_2_y9_1, TQGELFLLLDSR_2_y10_1, TQGELFLLLDSR_2_y4_1, TQGELFLLLDSR_2_y5_1, TQGELFLLLDSR_2_y7_1, VIGQDSSEIHFK_2_y10_1, VIGQDSSEIHFK_2_y3_1, VIGQDSSEIHFK_2_y4_1, VIGQDSSEIHFK_2_y6_1, VIGQDSSEIHFK_2_y7_1, VIGQDSSEIHFK_2_y8_1, QSQLQELILQQIAFK_2_y10_1, QSQLQELILQQIAFK_2_y5_1, QSQLQELILQQIAFK_2_y6_1, QSQLQELILQQIAFK_2_y7_1, QSQLQELILQQIAFK_2_y8_1, SVGDGETVEFDVVEGEK_2_y10_1, SVGDGETVEFDVVEGEK_2_y11_1, SVGDGETVEFDVVEGEK_2_y5_1, SVGDGETVEFDVVEGEK_2_y6_1, SVGDGETVEFDVVEGEK_2_y7_1, SVGDGETVEFDVVEGEK_2_y8_1, TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, SICEVLDLER_2_y3_1, SICEVLDLER_2_y5_1, SICEVLDLER_2_y6_1, SICEVLDLER_2_y7_1, SICEVLDLER_2_y8_1, VYENYPTYDLTER_2_y10_1, VYENYPTYDLTER_2_y3_1, VYENYPTYDLTER_2_y4_1, VYENYPTYDLTER_2_y5_1, VYENYPTYDLTER_2_y7_1, VYENYPTYDLTER_2_y9_1, EAHQLFLEPEVLDPESVELK_2_y12_1, EAHQLFLEPEVLDPESVELK_2_y3_1, EAHQLFLEPEVLDPESVELK_2_y4_1, EAHQLFLEPEVLDPESVELK_2_y5_1, EAHQLFLEPEVLDPESVELK_2_y7_1, EAHQLFLEPEVLDPESVELK_2_y8_1, LIADVAPSAIR_2_y5_1, LIADVAPSAIR_2_y6_1, LIADVAPSAIR_2_y7_1, LIADVAPSAIR_2_y8_1, LIADVAPSAIR_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_1, ISVATGALEAAQGSK_2_y11_1, ISVATGALEAAQGSK_2_y12_1, ISVATGALEAAQGSK_2_y5_1, ISVATGALEAAQGSK_2_y6_1, ISVATGALEAAQGSK_2_y8_1, ISVATGALEAAQGSK_2_y9_1, SPAFVQLAPLSSK_2_y10_1, SPAFVQLAPLSSK_2_y5_1, SPAFVQLAPLSSK_2_y6_1, SPAFVQLAPLSSK_2_y7_1, SPAFVQLAPLSSK_2_y8_1, SPAFVQLAPLSSK_2_y9_1, SPISVPGGSALISNLGK_2_y10_1, SPISVPGGSALISNLGK_2_y11_1, SPISVPGGSALISNLGK_2_y12_1, SPISVPGGSALISNLGK_2_y5_1, SPISVPGGSALISNLGK_2_y6_1, GPLTVEETPR_2_y4_1, GPLTVEETPR_2_y5_1, GPLTVEETPR_2_y6_1, GPLTVEETPR_2_y7_1, GPLTVEETPR_2_y8_1, ADTGLETSTR_2_y3_1, ADTGLETSTR_2_y4_1, ADTGLETSTR_2_y5_1, ADTGLETSTR_2_y6_1, ADTGLETSTR_2_y7_1, ADTGLETSTR_2_y8_1, LLLAVFVTPLTDLR_2_y10_1, LLLAVFVTPLTDLR_2_y11_1, LLLAVFVTPLTDLR_2_y6_1, LLLAVFVTPLTDLR_2_y8_1, LLLAVFVTPLTDLR_2_y9_1, NCAILIENDQSISR_2_y3_1, NCAILIENDQSISR_2_y4_1, NCAILIENDQSISR_2_y5_1, FGYVDFESAEDLEK_2_y10_1, FGYVDFESAEDLEK_2_y11_1, FGYVDFESAEDLEK_2_y7_1, FGYVDFESAEDLEK_2_y8_1, FGYVDFESAEDLEK_2_y9_1, GLSEDTTEETLK_2_y10_1, GLSEDTTEETLK_2_y4_1, GLSEDTTEETLK_2_y6_1, GLSEDTTEETLK_2_y7_1, GLSEDTTEETLK_2_y8_1, ALPNNTSSSPQPK_2_y10_1, ALPNNTSSSPQPK_2_y11_1, ALPNNTSSSPQPK_2_y6_1, ALPNNTSSSPQPK_2_y7_1, ALPNNTSSSPQPK_2_y8_1, ALPNNTSSSPQPK_2_y9_1, ELNEALELK_2_y4_1, ELNEALELK_2_y5_1, ELNEALELK_2_y6_1, ELNEALELK_2_y7_1, SVTCTYSPALNK_2_y10_1, SVTCTYSPALNK_2_y3_1, SVTCTYSPALNK_2_y5_1, SVTCTYSPALNK_2_y7_1, SVTCTYSPALNK_2_y8_1, SVTCTYSPALNK_2_y9_1, SLQELFLAHILSPWGAEVK_2_y10_1, SLQELFLAHILSPWGAEVK_2_y12_1, SLQELFLAHILSPWGAEVK_2_y7_1, SLQELFLAHILSPWGAEVK_2_y8_1, SLQELFLAHILSPWGAEVK_2_y9_1, AEDNADTLALVFEAPNQEK_2_y10_1, AEDNADTLALVFEAPNQEK_2_y11_1, AEDNADTLALVFEAPNQEK_2_y5_1, AEDNADTLALVFEAPNQEK_2_y6_1, AEDNADTLALVFEAPNQEK_2_y7_1, AEDNADTLALVFEAPNQEK_2_y8_1, AEDNADTLALVFEAPNQEK_2_y9_1, DLSHIGDAVVISCAK_2_y10_1, DLSHIGDAVVISCAK_2_y11_1, DLSHIGDAVVISCAK_2_y4_1, DLSHIGDAVVISCAK_2_y5_1, DLSHIGDAVVISCAK_2_y6_1, DLSHIGDAVVISCAK_2_y7_1, DLSHIGDAVVISCAK_2_y8_1, DLSHIGDAVVISCAK_2_y9_1, LGLTEDQFIR_2_y3_1, LGLTEDQFIR_2_y4_1, LGLTEDQFIR_2_y5_1, LGLTEDQFIR_2_y6_1, LGLTEDQFIR_2_y7_1, ATQQQHDFTLTQTADGR_2_y10_1, ATQQQHDFTLTQTADGR_2_y11_1, ATQQQHDFTLTQTADGR_2_y12_1, ATQQQHDFTLTQTADGR_2_y7_1, TVGALQVLGTEAQSSLLK_2_y10_1, TVGALQVLGTEAQSSLLK_2_y11_1, TVGALQVLGTEAQSSLLK_2_y12_1, TVGALQVLGTEAQSSLLK_2_y13_1, TVGALQVLGTEAQSSLLK_2_y7_1, TVGALQVLGTEAQSSLLK_2_y9_1, STAVTTSSAK_2_y2_1, STAVTTSSAK_2_y3_1, STAVTTSSAK_2_y4_1, STAVTTSSAK_2_y5_1, STAVTTSSAK_2_y7_1, GWFDAEGQALDGVSISDLK_2_y10_1, GWFDAEGQALDGVSISDLK_2_y11_1, GWFDAEGQALDGVSISDLK_2_y13_1, GWFDAEGQALDGVSISDLK_2_y6_1, GWFDAEGQALDGVSISDLK_2_y9_1, VIDQQNGLYR_2_y2_1, VIDQQNGLYR_2_y4_1, VIDQQNGLYR_2_y5_1, VIDQQNGLYR_2_y6_1, VIDQQNGLYR_2_y7_1, VIDQQNGLYR_2_y8_1, VVPIASLTPYQSK_2_y11_1, VVPIASLTPYQSK_2_y5_1, VVPIASLTPYQSK_2_y6_1, VVPIASLTPYQSK_2_y8_1, VVPIASLTPYQSK_2_y9_1, AEEVATFFAK_2_y3_1, AEEVATFFAK_2_y4_1, AEEVATFFAK_2_y7_1, AEEVATFFAK_2_y8_1, ELTAPDENIPAK_2_y10_1, ELTAPDENIPAK_2_y6_1, ELTAPDENIPAK_2_y7_1, ELTAPDENIPAK_2_y9_1, GPVFAPPYEPLPENVK_2_y10_1, GPVFAPPYEPLPENVK_2_y11_1, GPVFAPPYEPLPENVK_2_y12_1, GPVFAPPYEPLPENVK_2_y5_1, GPVFAPPYEPLPENVK_2_y7_1, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_1, AGLNGLQLAVLAR_2_y4_1, AGLNGLQLAVLAR_2_y5_1, AGLNGLQLAVLAR_2_y6_1, AGLNGLQLAVLAR_2_y7_1, AGLNGLQLAVLAR_2_y8_1, AGLNGLQLAVLAR_2_y9_1, NHQGPLPPVPLHLR_2_y10_1, NHQGPLPPVPLHLR_2_y5_1, NHQGPLPPVPLHLR_2_y6_1, NHQGPLPPVPLHLR_2_y7_1, NHQGPLPPVPLHLR_2_y8_1, TILFIDEIHR_2_y5_1, TILFIDEIHR_2_y6_1, TILFIDEIHR_2_y7_1, TILFIDEIHR_2_y8_1, LVVIDSVAAPFR_2_y3_1, LVVIDSVAAPFR_2_y4_1, LVVIDSVAAPFR_2_y5_1, LVVIDSVAAPFR_2_y6_1, LVVIDSVAAPFR_2_y7_1, ANPQVGVAFPHIK_2_y4_1, ANPQVGVAFPHIK_2_y5_1, ANPQVGVAFPHIK_2_y6_1, ANPQVGVAFPHIK_2_y8_1, ANPQVGVAFPHIK_2_y9_1, SQLDIIIHSLK_2_y3_1, SQLDIIIHSLK_2_y4_1, SQLDIIIHSLK_2_y5_1, SQLDIIIHSLK_2_y6_1, SQLDIIIHSLK_2_y8_1, SQLDIIIHSLK_2_y9_1, ELVYPPDYNPEGK_2_y10_1, ELVYPPDYNPEGK_2_y4_1, ELVYPPDYNPEGK_2_y6_1, ELVYPPDYNPEGK_2_y8_1, SDSFENPVLQQHFR_2_y3_1, SDSFENPVLQQHFR_2_y4_1, SDSFENPVLQQHFR_2_y5_1, SDSFENPVLQQHFR_2_y6_1, SDSFENPVLQQHFR_2_y8_1, SDSFENPVLQQHFR_2_y9_1) that are missing intensities for an entire condition.  Intensities in these conditions have been imputed with the minimum intensity across all samples.
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
error : can't analyze CAF1B for comparison.
Testing a comparison for protein  CHD4 ( 3  of  38 )
error : can't analyze CHD4 for comparison.
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
error : can't analyze HCFC1 for comparison.
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
error : can't analyze MBD3 for comparison.
Testing a comparison for protein  MDC1 ( 10  of  38 )
error : can't analyze MDC1 for comparison.
Testing a comparison for protein  MED4 ( 11  of  38 )
error : can't analyze MED4 for comparison.
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
error : can't analyze MSH2 for comparison.
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
error : can't analyze P53 for comparison.
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
error : can't analyze PCNA for comparison.
Testing a comparison for protein  POLD1 ( 20  of  38 )
error : can't analyze POLD1 for comparison.
Testing a comparison for protein  POLR2E ( 21  of  38 )
error : can't analyze POLR2E for comparison.
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
error : can't analyze RBBP4 for comparison.
Testing a comparison for protein  RPA1 ( 25  of  38 )
error : can't analyze RPA1 for comparison.
Testing a comparison for protein  SKIV2 ( 26  of  38 )
error : can't analyze SKIV2 for comparison.
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
error : can't analyze TFDP1 for comparison.
Testing a comparison for protein  TOP1 ( 32  of  38 )
error : can't analyze TOP1 for comparison.
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
error : can't analyze WRNIP1 for comparison.
Testing a comparison for protein  XRCC3 ( 35  of  38 )
error : can't analyze XRCC3 for comparison.
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 50 or more warnings (use warnings() to see the first 50)
-------------------------------------
Thu Jan 16 13:42:45 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
-------------------------------------
Thu Jan 16 13:44:32 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
The features that are missing intensities for an entire condition in Protein will be removed for fitting the model.
Testing a comparison for protein   ( 1  of  0 )
Protein BLM has only single transition, the simplied model is fitted
error : can't analyze BLM for comparison.
Error in `$<-.data.frame`(`*tmp*`, "residuals", value = NA) : 
  replacement has 1 row, data has 0
Calls: groupComparison -> $<- -> $<-.data.frame
Execution halted
-------------------------------------
Thu Jan 16 13:45:51 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
-------------------------------------
Thu Jan 16 13:49:31 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Error in heatmap.2(as.matrix(obj), col = my.colors, Colv = FALSE, dendrogram = "none",  : 
  `x' must have at least 2 rows and 2 columns
Calls: groupComparisonPlots -> heatmap.2
Execution halted
-------------------------------------
Thu Jan 16 13:50:13 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
-------------------------------------
Fri Jan 17 10:54:39 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
error : can't analyze BLM for comparison.
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
error : can't analyze H2AX for comparison.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 16 warnings (use warnings() to see them)
Testing a comparison for protein  BLM ( 1  of  38 )
error : can't analyze BLM for comparison.
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
error : can't analyze H2AX for comparison.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 16 warnings (use warnings() to see them)
null device 
          1 
null device 
          1 
-------------------------------------
Fri Jan 17 10:58:09 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
-------------------------------------
Fri Jan 17 10:59:05 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
error : can't analyze BLM for comparison.
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
error : can't analyze H2AX for comparison.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 16 warnings (use warnings() to see them)
Testing a comparison for protein  BLM ( 1  of  38 )
error : can't analyze BLM for comparison.
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
error : can't analyze H2AX for comparison.
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
There were 16 warnings (use warnings() to see them)
null device 
          1 
null device 
          1 
-------------------------------------
Fri Jan 17 11:04:02 PST 2014
Running RemoveUnrefinedTransitions.py on input_manually_fixed.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
                       
  Summary of Features :
                         count
# of Protein                38
# of Peptides/Protein      1-4
# of Transitions/Peptide   3-8
                      
  Summary of Samples :
                           CPT1 DMSO
# of MS runs                 33   33
# of Biological Replicates    3    4
# of Technical Replicates    11    8

 Summary of Missingness :

  # transitions are completely missing in one condition: 0

  # run with 75% missing observations: 0

Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
Testing a comparison for protein  BLM ( 1  of  38 )
Testing a comparison for protein  CAF1B ( 2  of  38 )
Testing a comparison for protein  CHD4 ( 3  of  38 )
Testing a comparison for protein  DEK ( 4  of  38 )
Testing a comparison for protein  FEN1 ( 5  of  38 )
Testing a comparison for protein  H2AX ( 6  of  38 )
Testing a comparison for protein  HCFC1 ( 7  of  38 )
Testing a comparison for protein  HDAC1 ( 8  of  38 )
Testing a comparison for protein  MBD3 ( 9  of  38 )
Testing a comparison for protein  MDC1 ( 10  of  38 )
Testing a comparison for protein  MED4 ( 11  of  38 )
Testing a comparison for protein  MRE11 ( 12  of  38 )
Testing a comparison for protein  MSH2 ( 13  of  38 )
Testing a comparison for protein  MTA2 ( 14  of  38 )
Testing a comparison for protein  NBN ( 15  of  38 )
Testing a comparison for protein  NUCL ( 16  of  38 )
Testing a comparison for protein  P53 ( 17  of  38 )
Testing a comparison for protein  PARP1 ( 18  of  38 )
Testing a comparison for protein  PCNA ( 19  of  38 )
Testing a comparison for protein  POLD1 ( 20  of  38 )
Testing a comparison for protein  POLR2E ( 21  of  38 )
Testing a comparison for protein  PRKDC ( 22  of  38 )
Testing a comparison for protein  RALY ( 23  of  38 )
Testing a comparison for protein  RBBP4 ( 24  of  38 )
Testing a comparison for protein  RPA1 ( 25  of  38 )
Testing a comparison for protein  SKIV2 ( 26  of  38 )
Testing a comparison for protein  SPT16H ( 27  of  38 )
Testing a comparison for protein  SSRP1 ( 28  of  38 )
Testing a comparison for protein  SUMO1 ( 29  of  38 )
Testing a comparison for protein  TFAM ( 30  of  38 )
Testing a comparison for protein  TFDP1 ( 31  of  38 )
Testing a comparison for protein  TOP1 ( 32  of  38 )
Testing a comparison for protein  TRIM28 ( 33  of  38 )
Testing a comparison for protein  WRNIP1 ( 34  of  38 )
Testing a comparison for protein  XRCC3 ( 35  of  38 )
Testing a comparison for protein  XRCC5 ( 36  of  38 )
Testing a comparison for protein  XRCC6 ( 37  of  38 )
Testing a comparison for protein  YBOX1 ( 38  of  38 )
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
-------------------------------------
Fri Jan 17 13:42:49 PST 2014
Running RemoveUnrefinedTransitions.py on comp1_cpt1-dmso_msstatsinput-wrn_norm_01.csv to remove inconsistent transitions
Removed transition y7+ for CAF1B - VTLNTLQAWSK++
Removed transition y5+ for CAF1B - VTLNTLQAWSK++
Running MakePlots.R on refined.csv to perform R analysis and generate plots
Loading required package: plyr

Attaching package: 'reshape'

The following object is masked from 'package:plyr':

    rename, round_any

Loading required package: Rcpp
Loading required package: MSnbase
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, get,
    intersect, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: mzR

This is MSnbase version 1.9.8 
  Read '?MSnbase' and references therein for information
  about the package and how getting started.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning message:
replacing previous import 'fortify' when loading 'ggplot2' 
Missing feature intensities should be given by 'NA' in the abundance column.
Error in dataProcess(csvData, normalization = FALSE, address = "msstats_out/") : 
  
Execution halted
