xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

Author
Christian Stratowa, Vienna, Austria
Date of publication
None
Maintainer
Christian Stratowa <cstrato@aon.at>
License
GPL (>= 2.0)
Version
1.34.0

View on Bioconductor

Man pages

addData-methods
Import additional CEL files into a DataTreeSet
AffyRNAdeg
Functions to assess RNA Degradation.
AnalysisTreeSet-class
Class AnalysisTreeSet
attachBgrd-methods
Attach/Remove Background Intensities
attachCall-methods
Attach/Remove Detecion Call Measures
attachData-methods
Attach/Remove Data
attachDataXY-methods
Attach/Remove (X,Y)-Coordinates
attachExpr-methods
Attach/Remove Expression Measures
attachInten-methods
Attach/Remove Intensities
attachMask-methods
Attach/Remove Scheme Mask
attachProbe-methods
Attach/Remove Probe Sequence and/or GC Content
attachUnitNames-methods
Attach/Remove Unit Names
bgcorrect
Background Correction
borderplot-methods
Plots of Border Elements
boxplot-methods
Box Plots
callFilter-methods
Detection Call Filter
callplot-methods
Barplot of Percent Present and Absent Calls.
CallTreeSet-class
Class CallTreeSet
coiplot-methods
Center-Of-Intensity QC Plots
corplot-methods
Array-Array Expression Level Correlation Plot
cvFilter-methods
Coefficient of Variation Filter
dabg.call
Detection Above Background Call
DataTreeSet-class
Class DataTreeSet
dfw
Distribution Free Weighted Expression Measure
diffFilter-methods
Difference Filter
existsROOTFile
Test for Existing ROOT File
exonLevel
Conversion of Parameter exonlevel to Integer
export
Export data as text files
export.filter
Export filter data as text files
export.root
Export data from ROOT file
express
Compute expression levels from raw data
exprs-methods
Get/Set Expression Values
ExprTreeSet-class
Class ExprTreeSet
extenPart
Get Extension of Tree Names
farms
Factor Analysis for Robust Microarray Summarization...
fcFilter-methods
Fold-Change Filter
Filter-class
Base Class Filter
FilterTreeSet-class
Class FilterTreeSet
firma
Finding Isoforms using Robust Multichip Analysis
firma.expr
Get Expression Levels from FIRMA
firma.score
Get Splice Score from FIRMA
fitQC
Functions for fitting probe-level models
fitRLM
Functions for fitting RMA as probe-level model
gapFilter-methods
Gap Filter
getChipName
Get Chip Name
getChipType
Get Chip Type
getDatatype
Get Data Type
getNameType
Get Chip Name and Type
getNumberTrees
Get Number of Trees
getProbeInfo
Get Probe Information
getTreeData-methods
Export Tree Data
getTreeNames
Get Tree Names
highFilter-methods
Upper Threshold Filter
hist-methods
Plot Density Estimate
image-methods
Display an Image
import.data
Import CEL files into a DataTreeSet
import.exon.scheme
Import CLF, PGF and annotation files into a SchemeTreeSet
import.expr.scheme
Import CDF, probe and annotation files into a SchemeTreeSet
import.genome.scheme
Import CLF, PGF and annotation files into a SchemeTreeSet
indexUnits-methods
Unit Locations
ini.call
Informative/Non-Informative Call
initialize-methods
Initialize Classes
intensity2GCplot-methods
Boxlot of Probe Intensities Stratified by GC Content.
intensity-methods
Get/Set Data Values
isROOTFile
Test for ROOT File
lowFilter-methods
Lower Threshold Filter
madFilter-methods
Median Absolute Deviation Filter
madplot-methods
Array-Array Expression Level Distance Plot
mas4
MAS 4.0 Expression Measure
mas5
MAS 5.0 Expression Measure
mas5.call
MAS 5.0 Absolute Detection Call
mboxplot-methods
Box Plots of Relative M Values
metaProbesets
Create MetaProbeset File for APT
mvaplot-methods
M vs A Plot
namePart
Get Tree Names w/o Extension
normalize
Normalization on Affymetrix Probe Level Data or on Expression...
NUSE
Normalized Unscaled Standard Errors (NUSE)
nuseplot-methods
Box Plots of Normalized Unscaled Standard Errors (NUSE)
pcaplot-methods
PCA Plot
plotBorder
Plots of Border Elements for Device
plotBoxplot
Box Plots for Device
plotCall
Barplot of Percent Present and Absent Calls for Device
plotCOI
Center-Of-Intensity QC Plots for Device
plotCorr
Array-Array Expression Level Correlation Plot for Device
plotDensity
Plot Density Estimate for Device
plotImage
Plot Image(s) for Device
plotIntensity2GC
Boxlot of Probe Intensities Stratified by GC Content for...
plotMA
MvA Scatter Plot for Device
plotMAD
Array-Array Expression Level Distance Plot for Device
plotNUSE
Box Plots of Normalized Unscaled Standard Errors (NUSE) for...
plotPCA
PCA Plot for Device
plotPM
Barplot of PM and MM Intensities for Device
plotProbeset
Plot of Probe Intensities for a Probeset for Device.
plotRLE
Box Plots of Relative Log Expression (RLE) for Device
plotVolcano
Volcano Plot
pm-methods
Methods for accessing perfect matches and mismatches
pmplot-methods
Barplot of PM and MM Intensities.
prefilter
Function for Applying a PreFilter to an ExprTreeSet
PreFilter-class
Class PreFilter
PreFilter-constructor
Constructor for Class PreFilter
presCall-methods
Get/Set Present Call Values
probeContentGC-methods
Get G/C Content for Probes
probeSequence-methods
Get Probe Sequence
probesetID2unitID-methods
Conversion between Probeset IDs and UnitIDs
probesetplot-methods
Plot of Probe Intensities for a Probeset.
ProcesSet-class
Class ProcesSet
ProjectInfo-class
Class ProjectInfo
ProjectInfo-constructor
Constructor for Class ProjectInfo
qualify
Probe Set Quality Control Functions
QualTreeSet-class
Class QualTreeSet
quantileFilter-methods
Quantile Filter
ratioFilter-methods
Ratio Filter
rawCELName-methods
Method for getting names of the raw CEL-files
RLE
Relative Log Expression (RLE)
rleplot-methods
Box Plots of Relative Log Expression (RLE)
rma
Robust Multi-Array Average Expression Measure
ROOT
ROOT An Object-Oriented Data Analysis Framework
root.browser-methods
Open the ROOT object browser
root.call
Create class CallTreeSet accessing ROOT detection call file
root.data
Create class DataTreeSet accessing ROOT data file
root.density
ROOT Density Plot
root.expr
Create class ExprTreeSet accessing ROOT expression file
root.graph1D
ROOT 1D-Graph
root.graph2D
ROOT 2D-Graph
root.hist1D
ROOT 1D-Histogram
root.hist2D
ROOT 2D-Histogram
root.hist3D
ROOT 3D-Histogram
root.image
ROOT Image
root.merge.data
Create class DataTreeSet by merging ROOT data files
root.mvaplot
ROOT M vs A Plot
root.profile
ROOT Profile Plot
root.scheme
Create class SchemeTreeSet accessing ROOT scheme file
SchemeTreeSet-class
Class SchemeTreeSet
summarize
Probe Set Summarizing Functions
symbol2unitID-methods
Conversion between Gene Symbols and UnitIDs
treeInfo-methods
Get UserInfo from ROOT Trees
TreeSet-class
Class TreeSet
trma
transposed Robust Multi-Array Average Expression Measure
type2Exten
Convert Method Type to Tree Extension
unifilter
Function for Applying an UniFilter to an ExprTreeSet
UniFilter-class
Class UniFilter
UniFilter-constructor
Constructor for Class UniFilter
unitestFilter-methods
Unitest Filter
uniTest-methods
A Two-Group Unitest
validCall-methods
Get Valid Detection Call Values
validData-methods
Extract Subset of Data
validExpr-methods
Get Valid Expression Levels
validSE-methods
Get Valid Standard Errors
validTreetype
Validate Tree Type
varFilter-methods
Variance Filter
volcanoplot-methods
Volcano Plot
xpsOptions
xps Options
xps-package
xps Package Overview
xpsQAReport
Create Quality Assessment Report.

Files in this package

xps/.BBSoptions
xps/ACKNOWLEDGMENT
xps/DESCRIPTION
xps/NAMESPACE
xps/NEWS
xps/R
xps/R/AffyRNAdeg.R
xps/R/Constructors.R
xps/R/TreeSetClasses.R
xps/R/bgcorrect.R
xps/R/dabg.call.R
xps/R/dfw.R
xps/R/export.R
xps/R/express.R
xps/R/farms.R
xps/R/filter.R
xps/R/firma.R
xps/R/fitQC.R
xps/R/import.R
xps/R/ini.call.R
xps/R/mas4.R
xps/R/mas5.R
xps/R/mas5.call.R
xps/R/methods.AnalysisTreeSet.R
xps/R/methods.CallTreeSet.R
xps/R/methods.DataTreeSet.R
xps/R/methods.ExprTreeSet.R
xps/R/methods.Filter.R
xps/R/methods.FilterTreeSet.R
xps/R/methods.PreFilter.R
xps/R/methods.ProcesSet.R
xps/R/methods.ProjectInfo.R
xps/R/methods.QualTreeSet.R
xps/R/methods.SchemeTreeSet.R
xps/R/methods.TreeSet.R
xps/R/methods.UniFilter.R
xps/R/normalize.R
xps/R/plot.R
xps/R/qualify.R
xps/R/rma.R
xps/R/root.files.R
xps/R/root.graphics.R
xps/R/summarize.R
xps/R/trma.R
xps/R/utils.R
xps/R/xpsQAReport.R
xps/R/zzz.R
xps/README
xps/build
xps/build/vignette.rds
xps/configure
xps/configure.in
xps/configure.vc10.win
xps/configure.win
xps/findroot.pl
xps/findvc.pl
xps/inst
xps/inst/ACKNOWLEDGMENT
xps/inst/CHANGELOG
xps/inst/QC
xps/inst/QC/QC.begin.Rnw
xps/inst/QC/QC.break.Rnw
xps/inst/QC/QC.call.Rnw
xps/inst/QC/QC.data.Rnw
xps/inst/QC/QC.end.Rnw
xps/inst/QC/QC.expr.Rnw
xps/inst/QC/QC.pseudo.fig.Rnw
xps/inst/QC/QC.pseudo.txt.Rnw
xps/inst/QC/QC.qual.Rnw
xps/inst/README
xps/inst/doc
xps/inst/doc/APTvsXPS.R
xps/inst/doc/APTvsXPS.Rnw
xps/inst/doc/APTvsXPS.pdf
xps/inst/doc/xps.R
xps/inst/doc/xps.Rnw
xps/inst/doc/xps.pdf
xps/inst/doc/xpsClasses.R
xps/inst/doc/xpsClasses.Rnw
xps/inst/doc/xpsClasses.pdf
xps/inst/doc/xpsPreprocess.R
xps/inst/doc/xpsPreprocess.Rnw
xps/inst/doc/xpsPreprocess.pdf
xps/inst/examples
xps/inst/examples/macro4XPS.C
xps/inst/examples/script4bestmatch.R
xps/inst/examples/script4exon.R
xps/inst/examples/script4schemes.R
xps/inst/examples/script4xps.R
xps/inst/examples/script4xps2apt.R
xps/inst/examples/script4xpsPreprocess.R
xps/inst/examples/updateAnnotation.R
xps/inst/raw
xps/inst/raw/TestA1.CEL
xps/inst/raw/TestA2.CEL
xps/inst/raw/TestB1.CEL
xps/inst/raw/TestB2.CEL
xps/inst/rootdata
xps/inst/rootdata/DataTest3_cel.root
xps/inst/rootdata/tmp_Test3RMA.root
xps/inst/rootsrc
xps/inst/rootsrc/macroDraw.C
xps/inst/rootsrc/macroDrawDensity.C
xps/inst/rootsrc/macroDrawImage.C
xps/inst/rootsrc/macroDrawLeaves.C
xps/inst/rootsrc/macroDrawProfilePlot.C
xps/inst/rootsrc/macroOpenBrowser.C
xps/inst/schemes
xps/inst/schemes/SchemeTest3.root
xps/man
xps/man/AffyRNAdeg.Rd
xps/man/AnalysisTreeSet-class.Rd
xps/man/CallTreeSet-class.Rd
xps/man/DataTreeSet-class.Rd
xps/man/ExprTreeSet-class.Rd
xps/man/Filter-class.Rd
xps/man/FilterTreeSet-class.Rd
xps/man/NUSE.Rd
xps/man/PreFilter-class.Rd
xps/man/PreFilter-constructor.Rd
xps/man/ProcesSet-class.Rd
xps/man/ProjectInfo-class.Rd
xps/man/ProjectInfo-constructor.Rd
xps/man/QualTreeSet-class.Rd
xps/man/RLE.Rd
xps/man/ROOT.Rd
xps/man/SchemeTreeSet-class.Rd
xps/man/TreeSet-class.Rd
xps/man/UniFilter-class.Rd
xps/man/UniFilter-constructor.Rd
xps/man/addData-methods.Rd
xps/man/attachBgrd-methods.Rd
xps/man/attachCall-methods.Rd
xps/man/attachData-methods.Rd
xps/man/attachDataXY-methods.Rd
xps/man/attachExpr-methods.Rd
xps/man/attachInten-methods.Rd
xps/man/attachMask-methods.Rd
xps/man/attachProbe-methods.Rd
xps/man/attachUnitNames-methods.Rd
xps/man/bgcorrect.Rd
xps/man/borderplot-methods.Rd
xps/man/boxplot-methods.Rd
xps/man/callFilter-methods.Rd
xps/man/callplot-methods.Rd
xps/man/coiplot-methods.Rd
xps/man/corplot-methods.Rd
xps/man/cvFilter-methods.Rd
xps/man/dabg.call.Rd
xps/man/dfw.Rd
xps/man/diffFilter-methods.Rd
xps/man/existsROOTFile.Rd
xps/man/exonLevel.Rd
xps/man/export.Rd
xps/man/export.filter.Rd
xps/man/export.root.Rd
xps/man/express.Rd
xps/man/exprs-methods.Rd
xps/man/extenPart.Rd
xps/man/farms.Rd
xps/man/fcFilter-methods.Rd
xps/man/firma.Rd
xps/man/firma.expr.Rd
xps/man/firma.score.Rd
xps/man/fitQC.Rd
xps/man/fitRLM.Rd
xps/man/gapFilter-methods.Rd
xps/man/getChipName.Rd
xps/man/getChipType.Rd
xps/man/getDatatype.Rd
xps/man/getNameType.Rd
xps/man/getNumberTrees.Rd
xps/man/getProbeInfo.Rd
xps/man/getTreeData-methods.Rd
xps/man/getTreeNames.Rd
xps/man/highFilter-methods.Rd
xps/man/hist-methods.Rd
xps/man/image-methods.Rd
xps/man/import.data.Rd
xps/man/import.exon.scheme.Rd
xps/man/import.expr.scheme.Rd
xps/man/import.genome.scheme.Rd
xps/man/indexUnits-methods.Rd
xps/man/ini.call.Rd
xps/man/initialize-methods.Rd
xps/man/intensity-methods.Rd
xps/man/intensity2GCplot-methods.Rd
xps/man/isROOTFile.Rd
xps/man/lowFilter-methods.Rd
xps/man/madFilter-methods.Rd
xps/man/madplot-methods.Rd
xps/man/mas4.Rd
xps/man/mas5.Rd
xps/man/mas5.call.Rd
xps/man/mboxplot-methods.Rd
xps/man/metaProbesets.Rd
xps/man/mvaplot-methods.Rd
xps/man/namePart.Rd
xps/man/normalize.Rd
xps/man/nuseplot-methods.Rd
xps/man/pcaplot-methods.Rd
xps/man/plotBorder.Rd
xps/man/plotBoxplot.Rd
xps/man/plotCOI.Rd
xps/man/plotCall.Rd
xps/man/plotCorr.Rd
xps/man/plotDensity.Rd
xps/man/plotImage.Rd
xps/man/plotIntensity2GC.Rd
xps/man/plotMA.Rd
xps/man/plotMAD.Rd
xps/man/plotNUSE.Rd
xps/man/plotPCA.Rd
xps/man/plotPM.Rd
xps/man/plotProbeset.Rd
xps/man/plotRLE.Rd
xps/man/plotVolcano.Rd
xps/man/pm-methods.Rd
xps/man/pmplot-methods.Rd
xps/man/prefilter.Rd
xps/man/presCall-methods.Rd
xps/man/probeContentGC-methods.Rd
xps/man/probeSequence-methods.Rd
xps/man/probesetID2unitID-methods.Rd
xps/man/probesetplot-methods.Rd
xps/man/qualify.Rd
xps/man/quantileFilter-methods.Rd
xps/man/ratioFilter-methods.Rd
xps/man/rawCELName-methods.Rd
xps/man/rleplot-methods.Rd
xps/man/rma.Rd
xps/man/root.browser-methods.Rd
xps/man/root.call.Rd
xps/man/root.data.Rd
xps/man/root.density.Rd
xps/man/root.expr.Rd
xps/man/root.graph1D.Rd
xps/man/root.graph2D.Rd
xps/man/root.hist1D.Rd
xps/man/root.hist2D.Rd
xps/man/root.hist3D.Rd
xps/man/root.image.Rd
xps/man/root.merge.data.Rd
xps/man/root.mvaplot.Rd
xps/man/root.profile.Rd
xps/man/root.scheme.Rd
xps/man/summarize.Rd
xps/man/symbol2unitID-methods.Rd
xps/man/treeInfo-methods.Rd
xps/man/trma.Rd
xps/man/type2Exten.Rd
xps/man/uniTest-methods.Rd
xps/man/unifilter.Rd
xps/man/unitestFilter-methods.Rd
xps/man/validCall-methods.Rd
xps/man/validData-methods.Rd
xps/man/validExpr-methods.Rd
xps/man/validSE-methods.Rd
xps/man/validTreetype.Rd
xps/man/varFilter-methods.Rd
xps/man/volcanoplot-methods.Rd
xps/man/xps-package.Rd
xps/man/xpsOptions.Rd
xps/man/xpsQAReport.Rd
xps/src
xps/src/Makefile
xps/src/Makefile.arch
xps/src/Makefile.vc10.win
xps/src/Makefile.win
xps/src/Makefile.win32
xps/src/Makefile.winMD
xps/src/Makefile.winMT
xps/src/Makefile.winVC9
xps/src/RconfigR.h
xps/src/RdpqR.h
xps/src/RmathR.h
xps/src/RnmathR.h
xps/src/StatUtils.cxx
xps/src/StatUtils.h
xps/src/StatUtilsLinkDef.h
xps/src/TMLMath.cxx
xps/src/TMLMath.h
xps/src/TStat.cxx
xps/src/TStat.h
xps/src/XPSAnalysis.cxx
xps/src/XPSAnalysis.h
xps/src/XPSAnalyzer.cxx
xps/src/XPSAnalyzer.h
xps/src/XPSBase.cxx
xps/src/XPSBase.h
xps/src/XPSData.cxx
xps/src/XPSData.h
xps/src/XPSDataTypes.cxx
xps/src/XPSDataTypes.h
xps/src/XPSFilter.cxx
xps/src/XPSFilter.h
xps/src/XPSHybridizer.cxx
xps/src/XPSHybridizer.h
xps/src/XPSNormalizer.cxx
xps/src/XPSNormalizer.h
xps/src/XPSNormation.cxx
xps/src/XPSNormation.h
xps/src/XPSPreProcessing.cxx
xps/src/XPSPreProcessing.h
xps/src/XPSProcessing.cxx
xps/src/XPSProcessing.h
xps/src/XPSProjectHandler.cxx
xps/src/XPSProjectHandler.h
xps/src/XPSSchemes.cxx
xps/src/XPSSchemes.h
xps/src/XPSSelector.cxx
xps/src/XPSSelector.h
xps/src/XPSUtils.cxx
xps/src/XPSUtils.h
xps/src/rwrapper.cxx
xps/src/rwrapper.h
xps/src/xps.def
xps/src/xpsLinkDef.h
xps/vignettes
xps/vignettes/APTvsXPS.Rnw
xps/vignettes/BoxPlot_BgrdGC_bgrd.png
xps/vignettes/BoxPlot_BgrdMAS5_bgrd.png
xps/vignettes/BoxPlot_BgrdRMA.png
xps/vignettes/BoxPlot_BgrdRMA_bgrd.png
xps/vignettes/BoxPlot_BgrdRMA_data.png
xps/vignettes/BoxPlot_DataU133P2.png
xps/vignettes/BoxPlot_ExprDFW.png
xps/vignettes/BoxPlot_ExprFARMS.png
xps/vignettes/BoxPlot_ExprMedpol.png
xps/vignettes/BoxPlot_ExprTukey.png
xps/vignettes/BoxPlot_NormQuant.png
xps/vignettes/BoxPlot_NormSup_BgrdMAS.png
xps/vignettes/BoxPlot_NrmExpMean.png
xps/vignettes/Corrplot_legend.png
xps/vignettes/DensityPlot.png
xps/vignettes/DensityPlotRMA.png
xps/vignettes/DensityPlot_BgrdGC_pm.png
xps/vignettes/DensityPlot_BgrdMAS5_both.png
xps/vignettes/DensityPlot_BgrdRMA.png
xps/vignettes/DensityPlot_DataU133P2.png
xps/vignettes/DensityPlot_ExprDFW.png
xps/vignettes/DensityPlot_ExprFARMS.png
xps/vignettes/DensityPlot_ExprMedpol.png
xps/vignettes/DensityPlot_ExprTukey.png
xps/vignettes/DensityPlot_NormQuant.png
xps/vignettes/DensityPlot_NormSup_BgrdMAS.png
xps/vignettes/DensityPlot_NrmExpMean.png
xps/vignettes/Graph2D.png
xps/vignettes/Graph2DRMA.png
xps/vignettes/Histogram2DRMA.png
xps/vignettes/Histogram2DRMAsurf2.png
xps/vignettes/Histogram3D.png
xps/vignettes/Histogram3DRMA.png
xps/vignettes/Histogram3DRMArotated.png
xps/vignettes/Histogram3Drotated.png
xps/vignettes/HuExon_Diff_XPS_APT_DABG_pval_ps.png
xps/vignettes/HuExon_XPS_APT_MedPol_MvA.png
xps/vignettes/HuExon_XPS_APT_MedPol_MvA_ps.png
xps/vignettes/HuExon_XPS_APT_MedPol_MvA_tc.png
xps/vignettes/HuExon_XPS_APT_RMA_MvA.png
xps/vignettes/HuExon_XPS_APT_RMA_MvA_ps.png
xps/vignettes/HuExon_XPS_APT_RMA_MvA_tc.png
xps/vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_ps.png
xps/vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_tc.png
xps/vignettes/HuGeneDiff_XPS_APT_DABG_pval_tc_r4.png
xps/vignettes/HuGene_Diff_XPS_APT_DABG_pval.png
xps/vignettes/HuGene_Diff_XPS_DABG_MAS5_pval.png
xps/vignettes/HuGene_XPS_APT_MedPol_MvA.png
xps/vignettes/HuGene_XPS_APT_MedPol_MvA_tc_r4.png
xps/vignettes/HuGene_XPS_APT_RMA_MvA.png
xps/vignettes/HuGene_XPS_APT_RMA_MvA_ps_r4.png
xps/vignettes/HuGene_XPS_APT_RMA_MvA_tc_r4.png
xps/vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_ps_r4.png
xps/vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_tc_r4.png
xps/vignettes/Image.png
xps/vignettes/ImageZoom.png
xps/vignettes/Image_BgrdGC_bgrd4.png
xps/vignettes/Image_BgrdMAS4_bgrd4.png
xps/vignettes/Image_BgrdMAS5_8x8_bgrd4.png
xps/vignettes/Image_BgrdMAS5_bgrd4.png
xps/vignettes/Image_BgrdMAS8x8x_bgrd4.png
xps/vignettes/Image_BgrdRMA_bgrd4.png
xps/vignettes/Image_BgrdRMA_data4.png
xps/vignettes/MADplot_legend.png
xps/vignettes/MvAPlot.png
xps/vignettes/ProfileExonRMA.png
xps/vignettes/ScatterPlot_ExprDFW_BrABrB.png
xps/vignettes/ScatterPlot_ExprDFW_BrAPrA.png
xps/vignettes/ScatterPlot_ExprFARMS_BrABrB.png
xps/vignettes/ScatterPlot_ExprFARMS_BrAPrA.png
xps/vignettes/ScatterPlot_ExprMedpol_BrABrB.png
xps/vignettes/ScatterPlot_ExprMedpol_BrAPrA.png
xps/vignettes/ScatterPlot_ExprTukey_BrABrB.png
xps/vignettes/ScatterPlot_ExprTukey_BrAPrA.png
xps/vignettes/ScatterPlot_NormQuant_PM_BrABrB.png
xps/vignettes/ScatterPlot_NormQuant_PM_BrAPrA.png
xps/vignettes/U133P2_APT_PLIER_MvA.png
xps/vignettes/U133P2_APT_PLIER_Scatter.png
xps/vignettes/U133P2_APT_RMA_MvA.png
xps/vignettes/U133P2_APT_RMA_RMAsketch_MvA.png
xps/vignettes/U133P2_Diff_XPS_AFFY_MAS5_pval.png
xps/vignettes/U133P2_XPS_AFFY_APT_RMA.png
xps/vignettes/U133P2_XPS_AFFY_EC_APT_MAS5_pval.png
xps/vignettes/U133P2_XPS_APT_EC_AFFY_MAS5_MvA_3x2.png
xps/vignettes/U133P2_XPS_APT_RMA_MvA.png
xps/vignettes/XPS_APT_HuExon_AdjPValue.png
xps/vignettes/XPS_APT_HuGene_PValue.png
xps/vignettes/XPS_U133P2_Gene_Exon_mean_dot.png
xps/vignettes/XPS_U133P2_HuGene_HuExon_logFC.png
xps/vignettes/xps.Rnw
xps/vignettes/xps.bib
xps/vignettes/xpsClasses.Rnw
xps/vignettes/xpsPreprocess.Rnw