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

NEWS
README
findvc.pl
configure.in
DESCRIPTION
ACKNOWLEDGMENT
.BBSoptions
configure.vc10.win
NAMESPACE
configure.win
INSTALL
configure
findroot.pl
inst/CHANGELOG
inst/README
inst/ACKNOWLEDGMENT
inst/INSTALL
inst/schemes/SchemeTest3.root
inst/rootdata/DataTest3_cel.root
inst/rootdata/tmp_Test3RMA.root
inst/doc/xpsClasses.R
inst/doc/xps.Rnw
inst/doc/APTvsXPS.Rnw
inst/doc/xpsPreprocess.Rnw
inst/doc/APTvsXPS.pdf inst/doc/xpsPreprocess.pdf
inst/doc/xpsClasses.Rnw
inst/doc/xpsPreprocess.R inst/doc/xpsClasses.pdf inst/doc/APTvsXPS.R inst/doc/xps.pdf inst/doc/xps.R
inst/QC/QC.begin.Rnw
inst/QC/QC.expr.Rnw
inst/QC/QC.pseudo.txt.Rnw
inst/QC/QC.qual.Rnw
inst/QC/QC.data.Rnw
inst/QC/QC.pseudo.fig.Rnw
inst/QC/QC.end.Rnw
inst/QC/QC.call.Rnw
inst/QC/QC.break.Rnw
inst/raw/TestB2.CEL
inst/raw/TestA2.CEL
inst/raw/TestA1.CEL
inst/raw/TestB1.CEL
inst/examples/script4schemes.R inst/examples/script4bestmatch.R inst/examples/script4xpsPreprocess.R inst/examples/updateAnnotation.R inst/examples/script4exon.R inst/examples/script4xps2apt.R inst/examples/script4xps.R
inst/examples/macro4XPS.C
inst/rootsrc/macroDrawDensity.C
inst/rootsrc/macroDrawLeaves.C
inst/rootsrc/macroOpenBrowser.C
inst/rootsrc/macroDrawProfilePlot.C
inst/rootsrc/macroDrawImage.C
inst/rootsrc/macroDraw.C
vignettes/HuGene_XPS_APT_RMA_MvA.png
vignettes/HuExon_XPS_APT_RMA_MvA.png
vignettes/Corrplot_legend.png
vignettes/U133P2_XPS_APT_RMA_MvA.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_ps_r4.png
vignettes/HuGene_XPS_APT_RMA_MvA_tc_r4.png
vignettes/Histogram3DRMArotated.png
vignettes/BoxPlot_NormQuant.png
vignettes/HuExon_XPS_APT_RMA_MvA_tc.png
vignettes/Histogram2DRMA.png
vignettes/HuExon_XPS_APT_MedPol_MvA_tc.png
vignettes/U133P2_APT_PLIER_Scatter.png
vignettes/BoxPlot_BgrdRMA.png
vignettes/XPS_APT_HuExon_AdjPValue.png
vignettes/DensityPlot_ExprDFW.png
vignettes/xps.Rnw
vignettes/XPS_U133P2_HuGene_HuExon_logFC.png
vignettes/HuGene_XPS_APT_MedPol_MvA_tc_r4.png
vignettes/DensityPlot_BgrdRMA.png
vignettes/Image_BgrdMAS4_bgrd4.png
vignettes/APTvsXPS.Rnw
vignettes/xpsPreprocess.Rnw
vignettes/ImageZoom.png
vignettes/MADplot_legend.png
vignettes/Image.png
vignettes/xpsClasses.Rnw
vignettes/DensityPlot_NormSup_BgrdMAS.png
vignettes/MvAPlot.png
vignettes/Image_BgrdMAS5_bgrd4.png
vignettes/U133P2_XPS_AFFY_APT_RMA.png
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_ps.png
vignettes/BoxPlot_NrmExpMean.png
vignettes/HuExon_XPS_APT_MedPol_MvA_ps.png
vignettes/BoxPlot_ExprMedpol.png
vignettes/ScatterPlot_ExprMedpol_BrAPrA.png
vignettes/HuGene_XPS_APT_RMA_MvA_ps_r4.png
vignettes/ScatterPlot_ExprTukey_BrAPrA.png
vignettes/HuExon_XPS_APT_MedPol_MvA.png
vignettes/U133P2_APT_RMA_RMAsketch_MvA.png
vignettes/HuGeneDiff_XPS_APT_DABG_pval_tc_r4.png
vignettes/ScatterPlot_NormQuant_PM_BrABrB.png
vignettes/HuGene_XPS_APT_MedPol_MvA.png
vignettes/DensityPlot_ExprFARMS.png
vignettes/ScatterPlot_NormQuant_PM_BrAPrA.png
vignettes/Image_BgrdMAS5_8x8_bgrd4.png
vignettes/ScatterPlot_ExprFARMS_BrAPrA.png
vignettes/HuExon_Diff_XPS_APT_DABG_pval_ps.png
vignettes/BoxPlot_DataU133P2.png
vignettes/ScatterPlot_ExprTukey_BrABrB.png
vignettes/DensityPlot_ExprMedpol.png
vignettes/XPS_APT_HuGene_PValue.png
vignettes/BoxPlot_BgrdGC_bgrd.png
vignettes/Histogram3DRMA.png
vignettes/Graph2DRMA.png
vignettes/HuExon_XPS_APT_RMA_MvA_ps.png
vignettes/U133P2_XPS_APT_EC_AFFY_MAS5_MvA_3x2.png
vignettes/U133P2_XPS_AFFY_EC_APT_MAS5_pval.png
vignettes/ScatterPlot_ExprFARMS_BrABrB.png
vignettes/DensityPlot_NrmExpMean.png
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_tc.png
vignettes/Histogram3Drotated.png
vignettes/DensityPlot_DataU133P2.png
vignettes/xps.bib
vignettes/ProfileExonRMA.png
vignettes/Image_BgrdRMA_data4.png
vignettes/XPS_U133P2_Gene_Exon_mean_dot.png
vignettes/DensityPlot_BgrdGC_pm.png
vignettes/ScatterPlot_ExprMedpol_BrABrB.png
vignettes/Image_BgrdMAS8x8x_bgrd4.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_tc_r4.png
vignettes/DensityPlot_NormQuant.png
vignettes/BoxPlot_ExprTukey.png
vignettes/BoxPlot_ExprFARMS.png
vignettes/Image_BgrdGC_bgrd4.png
vignettes/U133P2_Diff_XPS_AFFY_MAS5_pval.png
vignettes/Histogram3D.png
vignettes/DensityPlot.png
vignettes/ScatterPlot_ExprDFW_BrABrB.png
vignettes/BoxPlot_ExprDFW.png
vignettes/BoxPlot_BgrdRMA_data.png
vignettes/Histogram2DRMAsurf2.png
vignettes/Image_BgrdRMA_bgrd4.png
vignettes/BoxPlot_NormSup_BgrdMAS.png
vignettes/U133P2_APT_PLIER_MvA.png
vignettes/DensityPlot_BgrdMAS5_both.png
vignettes/DensityPlot_ExprTukey.png
vignettes/U133P2_APT_RMA_MvA.png
vignettes/Graph2D.png
vignettes/DensityPlotRMA.png
vignettes/HuGene_Diff_XPS_DABG_MAS5_pval.png
vignettes/HuGene_Diff_XPS_APT_DABG_pval.png
vignettes/BoxPlot_BgrdMAS5_bgrd.png
vignettes/ScatterPlot_ExprDFW_BrAPrA.png
vignettes/BoxPlot_BgrdRMA_bgrd.png
R/methods.UniFilter.R R/methods.Filter.R R/xpsQAReport.R R/express.R R/root.graphics.R R/summarize.R R/methods.ExprTreeSet.R R/rma.R R/ini.call.R R/zzz.R R/methods.ProcesSet.R R/export.R R/farms.R R/mas5.call.R R/plot.R R/methods.DataTreeSet.R R/utils.R R/filter.R R/methods.FilterTreeSet.R R/methods.TreeSet.R R/mas5.R R/normalize.R R/fitQC.R R/dfw.R R/methods.PreFilter.R R/firma.R R/AffyRNAdeg.R R/methods.SchemeTreeSet.R R/Constructors.R R/qualify.R R/root.files.R R/methods.CallTreeSet.R R/TreeSetClasses.R R/mas4.R R/trma.R R/methods.QualTreeSet.R R/methods.ProjectInfo.R R/bgcorrect.R R/methods.AnalysisTreeSet.R R/import.R R/dabg.call.R
src/XPSProcessing.cxx
src/TMLMath.cxx
src/XPSUtils.h
src/XPSHybridizer.cxx
src/Makefile.winMT
src/XPSNormation.cxx
src/xpsLinkDef.h
src/XPSPreProcessing.cxx
src/xps.def
src/TStat.h
src/rwrapper.cxx
src/rwrapper.h
src/Makefile
src/Makefile.arch
src/XPSUtils.cxx
src/XPSData.h
src/XPSPreProcessing.h
src/XPSFilter.cxx
src/StatUtils.h
src/XPSBase.cxx
src/StatUtils.cxx
src/TStat.cxx
src/XPSAnalyzer.cxx
src/XPSSelector.h
src/StatUtilsLinkDef.h
src/Makefile.winMD
src/XPSAnalysis.h
src/Makefile.vc10.win
src/Makefile.win32
src/XPSProjectHandler.cxx
src/XPSDataTypes.h
src/XPSFilter.h
src/XPSHybridizer.h
src/XPSSchemes.h
src/XPSNormation.h
src/RdpqR.h
src/XPSData.cxx
src/XPSNormalizer.h
src/XPSAnalyzer.h
src/Makefile.winVC9
src/XPSProcessing.h
src/XPSDataTypes.cxx
src/XPSSchemes.cxx
src/XPSAnalysis.cxx
src/XPSSelector.cxx
src/TMLMath.h
src/XPSBase.h
src/RmathR.h
src/RnmathR.h
src/RconfigR.h
src/XPSProjectHandler.h
src/Makefile.win
src/XPSNormalizer.cxx
man/xpsQAReport.Rd man/attachExpr-methods.Rd man/isROOTFile.Rd man/plotProbeset.Rd man/UniFilter-class.Rd man/root.browser-methods.Rd man/probeContentGC-methods.Rd man/indexUnits-methods.Rd man/plotCOI.Rd man/mas4.Rd man/pm-methods.Rd man/pmplot-methods.Rd man/qualify.Rd man/firma.Rd man/NUSE.Rd man/attachProbe-methods.Rd man/Filter-class.Rd man/metaProbesets.Rd man/FilterTreeSet-class.Rd man/attachInten-methods.Rd man/fitRLM.Rd man/dfw.Rd man/presCall-methods.Rd man/highFilter-methods.Rd man/varFilter-methods.Rd man/SchemeTreeSet-class.Rd man/ProjectInfo-constructor.Rd man/validSE-methods.Rd man/unifilter.Rd man/boxplot-methods.Rd man/corplot-methods.Rd man/plotRLE.Rd man/bgcorrect.Rd man/rawCELName-methods.Rd man/getNameType.Rd man/import.genome.scheme.Rd man/callFilter-methods.Rd man/plotIntensity2GC.Rd man/PreFilter-class.Rd man/quantileFilter-methods.Rd man/plotVolcano.Rd man/xps-package.Rd man/root.data.Rd man/root.merge.data.Rd man/farms.Rd man/attachUnitNames-methods.Rd man/madplot-methods.Rd man/validData-methods.Rd man/plotBoxplot.Rd man/plotPM.Rd man/validCall-methods.Rd man/root.scheme.Rd man/probesetID2unitID-methods.Rd man/attachData-methods.Rd man/attachCall-methods.Rd man/AnalysisTreeSet-class.Rd man/root.expr.Rd man/plotMAD.Rd man/import.exon.scheme.Rd man/getDatatype.Rd man/root.graph2D.Rd man/summarize.Rd man/rleplot-methods.Rd man/mas5.call.Rd man/attachMask-methods.Rd man/xpsOptions.Rd man/exonLevel.Rd man/export.root.Rd man/trma.Rd man/plotCall.Rd man/ini.call.Rd man/intensity-methods.Rd man/lowFilter-methods.Rd man/validExpr-methods.Rd man/madFilter-methods.Rd man/plotCorr.Rd man/dabg.call.Rd man/mboxplot-methods.Rd man/fitQC.Rd man/fcFilter-methods.Rd man/plotPCA.Rd man/UniFilter-constructor.Rd man/export.filter.Rd man/probesetplot-methods.Rd man/uniTest-methods.Rd man/type2Exten.Rd man/firma.score.Rd man/AffyRNAdeg.Rd man/plotNUSE.Rd man/root.call.Rd man/unitestFilter-methods.Rd man/ProjectInfo-class.Rd man/firma.expr.Rd man/coiplot-methods.Rd man/plotMA.Rd man/cvFilter-methods.Rd man/hist-methods.Rd man/borderplot-methods.Rd man/callplot-methods.Rd man/DataTreeSet-class.Rd man/CallTreeSet-class.Rd man/attachDataXY-methods.Rd man/getChipType.Rd man/export.Rd man/TreeSet-class.Rd man/plotDensity.Rd man/rma.Rd man/treeInfo-methods.Rd man/extenPart.Rd man/root.hist2D.Rd man/ExprTreeSet-class.Rd man/prefilter.Rd man/ratioFilter-methods.Rd man/getTreeNames.Rd man/nuseplot-methods.Rd man/gapFilter-methods.Rd man/getChipName.Rd man/import.data.Rd man/volcanoplot-methods.Rd man/pcaplot-methods.Rd man/root.graph1D.Rd man/mvaplot-methods.Rd man/ROOT.Rd man/initialize-methods.Rd man/ProcesSet-class.Rd man/attachBgrd-methods.Rd man/getNumberTrees.Rd man/diffFilter-methods.Rd man/plotBorder.Rd man/express.Rd man/probeSequence-methods.Rd man/validTreetype.Rd man/symbol2unitID-methods.Rd man/image-methods.Rd man/plotImage.Rd man/getTreeData-methods.Rd man/root.profile.Rd man/import.expr.scheme.Rd man/exprs-methods.Rd man/root.hist3D.Rd man/getProbeInfo.Rd man/addData-methods.Rd man/mas5.Rd man/root.hist1D.Rd man/namePart.Rd man/root.image.Rd man/PreFilter-constructor.Rd man/intensity2GCplot-methods.Rd man/root.density.Rd man/RLE.Rd man/QualTreeSet-class.Rd man/normalize.Rd man/root.mvaplot.Rd man/existsROOTFile.Rd
build/vignette.rds
xps documentation built on May 2, 2018, 2:33 a.m.