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

findvc.pl
findroot.pl
configure
.BBSoptions
DESCRIPTION
configure.vc10.win
README
NAMESPACE
NEWS
ACKNOWLEDGMENT
configure.in
INSTALL
configure.win
inst/ACKNOWLEDGMENT
inst/INSTALL
inst/README
inst/CHANGELOG
inst/examples/script4xpsPreprocess.R inst/examples/script4xps.R
inst/examples/macro4XPS.C
inst/examples/script4schemes.R inst/examples/script4exon.R inst/examples/script4bestmatch.R inst/examples/updateAnnotation.R inst/examples/script4xps2apt.R
inst/raw/TestA2.CEL
inst/raw/TestB1.CEL
inst/raw/TestB2.CEL
inst/raw/TestA1.CEL
inst/doc/xpsClasses.pdf inst/doc/xpsPreprocess.pdf
inst/doc/xpsPreprocess.Rnw
inst/doc/xpsClasses.Rnw
inst/doc/xpsPreprocess.R
inst/doc/xps.Rnw
inst/doc/xps.pdf inst/doc/xpsClasses.R
inst/doc/APTvsXPS.Rnw
inst/doc/APTvsXPS.pdf inst/doc/APTvsXPS.R inst/doc/xps.R
inst/QC/QC.begin.Rnw
inst/QC/QC.data.Rnw
inst/QC/QC.end.Rnw
inst/QC/QC.pseudo.txt.Rnw
inst/QC/QC.call.Rnw
inst/QC/QC.qual.Rnw
inst/QC/QC.pseudo.fig.Rnw
inst/QC/QC.expr.Rnw
inst/QC/QC.break.Rnw
inst/rootdata/tmp_Test3RMA.root
inst/rootdata/DataTest3_cel.root
inst/schemes/SchemeTest3.root
inst/rootsrc/macroDrawProfilePlot.C
inst/rootsrc/macroOpenBrowser.C
inst/rootsrc/macroDraw.C
inst/rootsrc/macroDrawLeaves.C
inst/rootsrc/macroDrawDensity.C
inst/rootsrc/macroDrawImage.C
src/TMLMath.cxx
src/XPSNormalizer.cxx
src/XPSPreProcessing.cxx
src/XPSAnalyzer.cxx
src/XPSData.h
src/XPSDataTypes.h
src/XPSProjectHandler.cxx
src/rwrapper.h
src/xpsLinkDef.h
src/rwrapper.cxx
src/XPSProcessing.cxx
src/Makefile.win
src/Makefile.winVC9
src/Makefile
src/RdpqR.h
src/XPSSchemes.cxx
src/Makefile.win32
src/XPSBase.cxx
src/TMLMath.h
src/XPSNormation.cxx
src/RconfigR.h
src/XPSUtils.h
src/XPSBase.h
src/XPSNormalizer.h
src/XPSAnalyzer.h
src/XPSData.cxx
src/XPSPreProcessing.h
src/StatUtilsLinkDef.h
src/StatUtils.cxx
src/XPSSelector.cxx
src/RnmathR.h
src/XPSFilter.h
src/XPSUtils.cxx
src/TStat.cxx
src/XPSSchemes.h
src/XPSDataTypes.cxx
src/Makefile.vc10.win
src/XPSProcessing.h
src/RmathR.h
src/xps.def
src/XPSHybridizer.cxx
src/Makefile.winMD
src/XPSProjectHandler.h
src/Makefile.arch
src/XPSAnalysis.cxx
src/XPSNormation.h
src/Makefile.winMT
src/TStat.h
src/XPSAnalysis.h
src/XPSSelector.h
src/XPSFilter.cxx
src/XPSHybridizer.h
src/StatUtils.h
build/vignette.rds
R/trma.R R/methods.CallTreeSet.R R/zzz.R R/bgcorrect.R R/qualify.R R/xpsQAReport.R R/methods.ExprTreeSet.R R/methods.FilterTreeSet.R R/methods.Filter.R R/ini.call.R R/filter.R R/dabg.call.R R/root.graphics.R R/methods.ProcesSet.R R/methods.ProjectInfo.R R/import.R R/methods.PreFilter.R R/farms.R R/methods.SchemeTreeSet.R R/summarize.R R/export.R R/mas5.call.R R/plot.R R/methods.TreeSet.R R/methods.AnalysisTreeSet.R R/normalize.R R/rma.R R/utils.R R/fitQC.R R/TreeSetClasses.R R/Constructors.R R/express.R R/methods.DataTreeSet.R R/dfw.R R/mas4.R R/AffyRNAdeg.R R/mas5.R R/methods.QualTreeSet.R R/root.files.R R/methods.UniFilter.R R/firma.R
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_tc.png
vignettes/ScatterPlot_ExprFARMS_BrABrB.png
vignettes/BoxPlot_DataU133P2.png
vignettes/MvAPlot.png
vignettes/BoxPlot_ExprTukey.png
vignettes/ScatterPlot_NormQuant_PM_BrAPrA.png
vignettes/BoxPlot_NormQuant.png
vignettes/HuGene_XPS_APT_MedPol_MvA.png
vignettes/BoxPlot_NormSup_BgrdMAS.png
vignettes/xps.Rnw
vignettes/HuExon_XPS_APT_RMA_MvA_tc.png
vignettes/DensityPlot_ExprFARMS.png
vignettes/ScatterPlot_ExprDFW_BrAPrA.png
vignettes/DensityPlot_DataU133P2.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_tc_r4.png
vignettes/U133P2_XPS_APT_EC_AFFY_MAS5_MvA_3x2.png
vignettes/ScatterPlot_ExprDFW_BrABrB.png
vignettes/HuExon_XPS_APT_MedPol_MvA_ps.png
vignettes/U133P2_APT_RMA_RMAsketch_MvA.png
vignettes/Histogram2DRMAsurf2.png
vignettes/ScatterPlot_NormQuant_PM_BrABrB.png
vignettes/DensityPlot.png
vignettes/ProfileExonRMA.png
vignettes/BoxPlot_BgrdRMA_data.png
vignettes/ScatterPlot_ExprFARMS_BrAPrA.png
vignettes/DensityPlot_BgrdGC_pm.png
vignettes/U133P2_Diff_XPS_AFFY_MAS5_pval.png
vignettes/DensityPlot_BgrdMAS5_both.png
vignettes/Corrplot_legend.png
vignettes/ScatterPlot_ExprTukey_BrAPrA.png
vignettes/xpsPreprocess.Rnw
vignettes/HuGene_XPS_APT_RMA_MvA_ps_r4.png
vignettes/ScatterPlot_ExprTukey_BrABrB.png
vignettes/XPS_APT_HuExon_AdjPValue.png
vignettes/Histogram3D.png
vignettes/Image_BgrdRMA_bgrd4.png
vignettes/Graph2D.png
vignettes/U133P2_APT_RMA_MvA.png
vignettes/Image_BgrdRMA_data4.png
vignettes/U133P2_APT_PLIER_MvA.png
vignettes/xps.bib
vignettes/MADplot_legend.png
vignettes/BoxPlot_BgrdGC_bgrd.png
vignettes/Image_BgrdMAS4_bgrd4.png
vignettes/XPS_U133P2_HuGene_HuExon_logFC.png
vignettes/BoxPlot_BgrdMAS5_bgrd.png
vignettes/DensityPlot_ExprMedpol.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_ps_r4.png
vignettes/ImageZoom.png
vignettes/Image_BgrdMAS5_bgrd4.png
vignettes/U133P2_APT_PLIER_Scatter.png
vignettes/Histogram3DRMA.png
vignettes/XPS_APT_HuGene_PValue.png
vignettes/APTvsXPS.Rnw
vignettes/Graph2DRMA.png
vignettes/BoxPlot_ExprMedpol.png
vignettes/DensityPlot_BgrdRMA.png
vignettes/HuExon_XPS_APT_MedPol_MvA_tc.png
vignettes/HuExon_XPS_APT_RMA_MvA_ps.png
vignettes/BoxPlot_BgrdRMA.png
vignettes/BoxPlot_NrmExpMean.png
vignettes/U133P2_XPS_APT_RMA_MvA.png
vignettes/HuExon_XPS_APT_MedPol_MvA.png
vignettes/DensityPlot_NormSup_BgrdMAS.png
vignettes/Histogram3Drotated.png
vignettes/DensityPlot_NrmExpMean.png
vignettes/Histogram3DRMArotated.png
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_ps.png
vignettes/XPS_U133P2_Gene_Exon_mean_dot.png
vignettes/HuExon_XPS_APT_RMA_MvA.png
vignettes/DensityPlot_ExprTukey.png
vignettes/DensityPlot_NormQuant.png
vignettes/HuGene_Diff_XPS_DABG_MAS5_pval.png
vignettes/HuGeneDiff_XPS_APT_DABG_pval_tc_r4.png
vignettes/HuGene_XPS_APT_RMA_MvA_tc_r4.png
vignettes/BoxPlot_ExprFARMS.png
vignettes/ScatterPlot_ExprMedpol_BrABrB.png
vignettes/DensityPlotRMA.png
vignettes/Image_BgrdMAS8x8x_bgrd4.png
vignettes/DensityPlot_ExprDFW.png
vignettes/ScatterPlot_ExprMedpol_BrAPrA.png
vignettes/HuGene_XPS_APT_MedPol_MvA_tc_r4.png
vignettes/Image_BgrdMAS5_8x8_bgrd4.png
vignettes/BoxPlot_ExprDFW.png
vignettes/Image.png
vignettes/HuExon_Diff_XPS_APT_DABG_pval_ps.png
vignettes/Histogram2DRMA.png
vignettes/HuGene_Diff_XPS_APT_DABG_pval.png
vignettes/HuGene_XPS_APT_RMA_MvA.png
vignettes/U133P2_XPS_AFFY_EC_APT_MAS5_pval.png
vignettes/xpsClasses.Rnw
vignettes/BoxPlot_BgrdRMA_bgrd.png
vignettes/Image_BgrdGC_bgrd4.png
vignettes/U133P2_XPS_AFFY_APT_RMA.png
man/dfw.Rd man/diffFilter-methods.Rd man/pmplot-methods.Rd man/DataTreeSet-class.Rd man/root.call.Rd man/attachInten-methods.Rd man/root.merge.data.Rd man/ExprTreeSet-class.Rd man/trma.Rd man/qualify.Rd man/nuseplot-methods.Rd man/AffyRNAdeg.Rd man/getDatatype.Rd man/attachCall-methods.Rd man/attachProbe-methods.Rd man/plotPM.Rd man/ROOT.Rd man/import.exon.scheme.Rd man/root.hist3D.Rd man/plotImage.Rd man/CallTreeSet-class.Rd man/firma.expr.Rd man/ProjectInfo-class.Rd man/root.graph1D.Rd man/root.expr.Rd man/plotPCA.Rd man/namePart.Rd man/intensity2GCplot-methods.Rd man/plotCall.Rd man/lowFilter-methods.Rd man/rma.Rd man/ini.call.Rd man/attachMask-methods.Rd man/normalize.Rd man/coiplot-methods.Rd man/fitQC.Rd man/getProbeInfo.Rd man/existsROOTFile.Rd man/getNumberTrees.Rd man/plotBoxplot.Rd man/plotBorder.Rd man/attachUnitNames-methods.Rd man/validTreetype.Rd man/dabg.call.Rd man/plotVolcano.Rd man/validCall-methods.Rd man/root.profile.Rd man/root.scheme.Rd man/callFilter-methods.Rd man/probesetplot-methods.Rd man/pcaplot-methods.Rd man/Filter-class.Rd man/fitRLM.Rd man/symbol2unitID-methods.Rd man/summarize.Rd man/madplot-methods.Rd man/plotIntensity2GC.Rd man/ProcesSet-class.Rd man/highFilter-methods.Rd man/farms.Rd man/isROOTFile.Rd man/indexUnits-methods.Rd man/import.data.Rd man/ProjectInfo-constructor.Rd man/corplot-methods.Rd man/NUSE.Rd man/type2Exten.Rd man/exonLevel.Rd man/metaProbesets.Rd man/root.hist2D.Rd man/attachBgrd-methods.Rd man/getChipName.Rd man/intensity-methods.Rd man/hist-methods.Rd man/plotCorr.Rd man/xpsQAReport.Rd man/UniFilter-class.Rd man/import.expr.scheme.Rd man/probeSequence-methods.Rd man/gapFilter-methods.Rd man/validData-methods.Rd man/attachDataXY-methods.Rd man/mvaplot-methods.Rd man/root.browser-methods.Rd man/PreFilter-class.Rd man/root.hist1D.Rd man/unifilter.Rd man/firma.Rd man/initialize-methods.Rd man/plotCOI.Rd man/root.data.Rd man/attachExpr-methods.Rd man/probesetID2unitID-methods.Rd man/image-methods.Rd man/express.Rd man/plotNUSE.Rd man/root.image.Rd man/probeContentGC-methods.Rd man/FilterTreeSet-class.Rd man/pm-methods.Rd man/cvFilter-methods.Rd man/QualTreeSet-class.Rd man/UniFilter-constructor.Rd man/xpsOptions.Rd man/rawCELName-methods.Rd man/PreFilter-constructor.Rd man/import.genome.scheme.Rd man/xps-package.Rd man/root.density.Rd man/unitestFilter-methods.Rd man/plotDensity.Rd man/plotMA.Rd man/exprs-methods.Rd man/SchemeTreeSet-class.Rd man/ratioFilter-methods.Rd man/root.mvaplot.Rd man/attachData-methods.Rd man/getNameType.Rd man/root.graph2D.Rd man/madFilter-methods.Rd man/quantileFilter-methods.Rd man/extenPart.Rd man/fcFilter-methods.Rd man/validSE-methods.Rd man/AnalysisTreeSet-class.Rd man/callplot-methods.Rd man/validExpr-methods.Rd man/plotRLE.Rd man/presCall-methods.Rd man/borderplot-methods.Rd man/bgcorrect.Rd man/varFilter-methods.Rd man/volcanoplot-methods.Rd man/mas5.Rd man/TreeSet-class.Rd man/prefilter.Rd man/getChipType.Rd man/export.filter.Rd man/firma.score.Rd man/addData-methods.Rd man/getTreeNames.Rd man/rleplot-methods.Rd man/RLE.Rd man/export.Rd man/mas5.call.Rd man/plotProbeset.Rd man/plotMAD.Rd man/getTreeData-methods.Rd man/boxplot-methods.Rd man/treeInfo-methods.Rd man/uniTest-methods.Rd man/export.root.Rd man/mboxplot-methods.Rd man/mas4.Rd
xps documentation built on Nov. 17, 2017, 1:17 p.m.