-------------------------------------
Tue Jan 21 16:59:00 PST 2014
Running MakePlots.R on  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 :
                           12h 1h 6h DMSO
# of MS runs                12 14 10   12
# of Biological Replicates   1  1  1    1
# of Technical Replicates   12 14 10   12

 Summary of Missingness :

  # transitions are completely missing in one condition: 37

    -> TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_1
  # 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 )
error : results of Protein  for comparison 1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 1h are NA because measurements in Group 1h are missing completely.
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 50 or more warnings (use warnings() to see the first 50)
There are 37 features (TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_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 )
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 )
There were 50 or more warnings (use warnings() to see the first 50)
null device 
          1 
Warning messages:
1: Removed 1 rows containing missing values (geom_segment). 
2: Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
-------------------------------------
Tue Jan 21 17:37:12 PST 2014
Running MakePlots.R on  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 :
                           12h 1h 6h DMSO
# of MS runs                12 14 10   12
# of Biological Replicates   1  1  1    1
# of Technical Replicates   12 14 10   12

 Summary of Missingness :

  # transitions are completely missing in one condition: 37

    -> TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_1
  # 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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 50 or more warnings (use warnings() to see the first 50)
There are 37 features (TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_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 )
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 )
There were 50 or more warnings (use warnings() to see the first 50)
null device 
          1 
Warning messages:
1: Removed 1 rows containing missing values (geom_segment). 
2: Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
-------------------------------------
Wed Feb 26 11:06:23 PST 2014
Running MakePlots.R on  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 :
                           12h 1h 6h DMSO
# of MS runs                12 14 10   12
# of Biological Replicates   1  1  1    1
# of Technical Replicates   12 14 10   12

 Summary of Missingness :

  # transitions are completely missing in one condition: 37

    -> TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_1
  # 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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 )
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 )
error : results of Protein  for comparison 0_1h are NA because measurements in Group 1h are missing completely.
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 50 or more warnings (use warnings() to see the first 50)
There are 37 features (TSSDNNVSVTNVSVAK_2_y10_1, TSSDNNVSVTNVSVAK_2_y5_1, TSSDNNVSVTNVSVAK_2_y6_1, TSSDNNVSVTNVSVAK_2_y7_1, TSSDNNVSVTNVSVAK_2_y8_1, TSSDNNVSVTNVSVAK_2_y9_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y10_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y11_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y12_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y13_1, LLGGVTIAQGGVLPNIQAVLLPK_2_y14_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, FQWDLNAWTK_2_y3_1, FQWDLNAWTK_2_y4_1, FQWDLNAWTK_2_y5_1, FQWDLNAWTK_2_y6_1, FQWDLNAWTK_2_y7_1, LDLDLTADSQPPVFK_2_y10_1, LDLDLTADSQPPVFK_2_y4_1, LDLDLTADSQPPVFK_2_y5_1, LDLDLTADSQPPVFK_2_y7_1, LDLDLTADSQPPVFK_2_y8_1, LDLDLTADSQPPVFK_2_y9_1, LSPPYSSPQEFAQDVGR_2_y10_1, LSPPYSSPQEFAQDVGR_2_y11_1, LSPPYSSPQEFAQDVGR_2_y12_1, LSPPYSSPQEFAQDVGR_2_y6_1, LSPPYSSPQEFAQDVGR_2_y7_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 )
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 )
There were 50 or more warnings (use warnings() to see the first 50)
null device 
          1 
Warning messages:
1: Removed 1 rows containing missing values (geom_segment). 
2: Removed 1 rows containing missing values (geom_segment). 
null device 
          1 
Warning message:
Removed 1 rows containing missing values (geom_segment). 
