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.

AuthorChristian Stratowa, Vienna, Austria
Date of publicationNone
MaintainerChristian Stratowa <cstrato@aon.at>
LicenseGPL (>= 2.0)
Version1.34.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.