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

.BBSoptions
ACKNOWLEDGMENT
DESCRIPTION
INSTALL
NAMESPACE
NEWS
R/AffyRNAdeg.R R/Constructors.R R/TreeSetClasses.R R/bgcorrect.R R/dabg.call.R R/dfw.R R/export.R R/express.R R/farms.R R/filter.R R/firma.R R/fitQC.R R/import.R R/ini.call.R R/mas4.R R/mas5.R R/mas5.call.R R/methods.AnalysisTreeSet.R R/methods.CallTreeSet.R R/methods.DataTreeSet.R R/methods.ExprTreeSet.R R/methods.Filter.R R/methods.FilterTreeSet.R R/methods.PreFilter.R R/methods.ProcesSet.R R/methods.ProjectInfo.R R/methods.QualTreeSet.R R/methods.SchemeTreeSet.R R/methods.TreeSet.R R/methods.UniFilter.R R/normalize.R R/plot.R R/qualify.R R/rma.R R/root.files.R R/root.graphics.R R/summarize.R R/trma.R R/utils.R R/xpsQAReport.R R/zzz.R
README
configure
configure.in
configure.vc10.win
configure.win
findroot.pl
findvc.pl
inst/ACKNOWLEDGMENT
inst/CHANGELOG
inst/INSTALL
inst/QC/QC.begin.Rnw
inst/QC/QC.break.Rnw
inst/QC/QC.call.Rnw
inst/QC/QC.data.Rnw
inst/QC/QC.end.Rnw
inst/QC/QC.expr.Rnw
inst/QC/QC.pseudo.fig.Rnw
inst/QC/QC.pseudo.txt.Rnw
inst/QC/QC.qual.Rnw
inst/README
inst/examples/macro4XPS.C
inst/examples/script4bestmatch.R inst/examples/script4exon.R inst/examples/script4schemes.R inst/examples/script4xps.R inst/examples/script4xps2apt.R inst/examples/script4xpsPreprocess.R inst/examples/updateAnnotation.R
inst/raw/TestA1.CEL
inst/raw/TestA2.CEL
inst/raw/TestB1.CEL
inst/raw/TestB2.CEL
inst/rootdata/DataTest3_cel.root
inst/rootdata/tmp_Test3RMA.root
inst/rootsrc/macroDraw.C
inst/rootsrc/macroDrawDensity.C
inst/rootsrc/macroDrawImage.C
inst/rootsrc/macroDrawLeaves.C
inst/rootsrc/macroDrawProfilePlot.C
inst/rootsrc/macroOpenBrowser.C
inst/schemes/SchemeTest3.root
man/AffyRNAdeg.Rd man/AnalysisTreeSet-class.Rd man/CallTreeSet-class.Rd man/DataTreeSet-class.Rd man/ExprTreeSet-class.Rd man/Filter-class.Rd man/FilterTreeSet-class.Rd man/NUSE.Rd man/PreFilter-class.Rd man/PreFilter-constructor.Rd man/ProcesSet-class.Rd man/ProjectInfo-class.Rd man/ProjectInfo-constructor.Rd man/QualTreeSet-class.Rd man/RLE.Rd man/ROOT.Rd man/SchemeTreeSet-class.Rd man/TreeSet-class.Rd man/UniFilter-class.Rd man/UniFilter-constructor.Rd man/addData-methods.Rd man/attachBgrd-methods.Rd man/attachCall-methods.Rd man/attachData-methods.Rd man/attachDataXY-methods.Rd man/attachExpr-methods.Rd man/attachInten-methods.Rd man/attachMask-methods.Rd man/attachProbe-methods.Rd man/attachUnitNames-methods.Rd man/bgcorrect.Rd man/borderplot-methods.Rd man/boxplot-methods.Rd man/callFilter-methods.Rd man/callplot-methods.Rd man/coiplot-methods.Rd man/corplot-methods.Rd man/cvFilter-methods.Rd man/dabg.call.Rd man/dfw.Rd man/diffFilter-methods.Rd man/existsROOTFile.Rd man/exonLevel.Rd man/export.Rd man/export.filter.Rd man/export.root.Rd man/express.Rd man/exprs-methods.Rd man/extenPart.Rd man/farms.Rd man/fcFilter-methods.Rd man/firma.Rd man/firma.expr.Rd man/firma.score.Rd man/fitQC.Rd man/fitRLM.Rd man/gapFilter-methods.Rd man/getChipName.Rd man/getChipType.Rd man/getDatatype.Rd man/getNameType.Rd man/getNumberTrees.Rd man/getProbeInfo.Rd man/getTreeData-methods.Rd man/getTreeNames.Rd man/highFilter-methods.Rd man/hist-methods.Rd man/image-methods.Rd man/import.data.Rd man/import.exon.scheme.Rd man/import.expr.scheme.Rd man/import.genome.scheme.Rd man/indexUnits-methods.Rd man/ini.call.Rd man/initialize-methods.Rd man/intensity-methods.Rd man/intensity2GCplot-methods.Rd man/isROOTFile.Rd man/lowFilter-methods.Rd man/madFilter-methods.Rd man/madplot-methods.Rd man/mas4.Rd man/mas5.Rd man/mas5.call.Rd man/mboxplot-methods.Rd man/metaProbesets.Rd man/mvaplot-methods.Rd man/namePart.Rd man/normalize.Rd man/nuseplot-methods.Rd man/pcaplot-methods.Rd man/plotBorder.Rd man/plotBoxplot.Rd man/plotCOI.Rd man/plotCall.Rd man/plotCorr.Rd man/plotDensity.Rd man/plotImage.Rd man/plotIntensity2GC.Rd man/plotMA.Rd man/plotMAD.Rd man/plotNUSE.Rd man/plotPCA.Rd man/plotPM.Rd man/plotProbeset.Rd man/plotRLE.Rd man/plotVolcano.Rd man/pm-methods.Rd man/pmplot-methods.Rd man/prefilter.Rd man/presCall-methods.Rd man/probeContentGC-methods.Rd man/probeSequence-methods.Rd man/probesetID2unitID-methods.Rd man/probesetplot-methods.Rd man/qualify.Rd man/quantileFilter-methods.Rd man/ratioFilter-methods.Rd man/rawCELName-methods.Rd man/rleplot-methods.Rd man/rma.Rd man/root.browser-methods.Rd man/root.call.Rd man/root.data.Rd man/root.density.Rd man/root.expr.Rd man/root.graph1D.Rd man/root.graph2D.Rd man/root.hist1D.Rd man/root.hist2D.Rd man/root.hist3D.Rd man/root.image.Rd man/root.merge.data.Rd man/root.mvaplot.Rd man/root.profile.Rd man/root.scheme.Rd man/summarize.Rd man/symbol2unitID-methods.Rd man/treeInfo-methods.Rd man/trma.Rd man/type2Exten.Rd man/uniTest-methods.Rd man/unifilter.Rd man/unitestFilter-methods.Rd man/validCall-methods.Rd man/validData-methods.Rd man/validExpr-methods.Rd man/validSE-methods.Rd man/validTreetype.Rd man/varFilter-methods.Rd man/volcanoplot-methods.Rd man/xps-package.Rd man/xpsOptions.Rd man/xpsQAReport.Rd
src/Makefile
src/Makefile.arch
src/Makefile.vc10.win
src/Makefile.win
src/Makefile.win32
src/Makefile.winMD
src/Makefile.winMT
src/Makefile.winVC9
src/RconfigR.h
src/RdpqR.h
src/RmathR.h
src/RnmathR.h
src/StatUtils.cxx
src/StatUtils.h
src/StatUtilsLinkDef.h
src/TMLMath.cxx
src/TMLMath.h
src/TStat.cxx
src/TStat.h
src/XPSAnalysis.cxx
src/XPSAnalysis.h
src/XPSAnalyzer.cxx
src/XPSAnalyzer.h
src/XPSBase.cxx
src/XPSBase.h
src/XPSData.cxx
src/XPSData.h
src/XPSDataTypes.cxx
src/XPSDataTypes.h
src/XPSFilter.cxx
src/XPSFilter.h
src/XPSHybridizer.cxx
src/XPSHybridizer.h
src/XPSNormalizer.cxx
src/XPSNormalizer.h
src/XPSNormation.cxx
src/XPSNormation.h
src/XPSPreProcessing.cxx
src/XPSPreProcessing.h
src/XPSProcessing.cxx
src/XPSProcessing.h
src/XPSProjectHandler.cxx
src/XPSProjectHandler.h
src/XPSSchemes.cxx
src/XPSSchemes.h
src/XPSSelector.cxx
src/XPSSelector.h
src/XPSUtils.cxx
src/XPSUtils.h
src/rwrapper.cxx
src/rwrapper.h
src/xps.def
src/xpsLinkDef.h
vignettes/APTvsXPS.Rnw
vignettes/BoxPlot_BgrdGC_bgrd.png
vignettes/BoxPlot_BgrdMAS5_bgrd.png
vignettes/BoxPlot_BgrdRMA.png
vignettes/BoxPlot_BgrdRMA_bgrd.png
vignettes/BoxPlot_BgrdRMA_data.png
vignettes/BoxPlot_DataU133P2.png
vignettes/BoxPlot_ExprDFW.png
vignettes/BoxPlot_ExprFARMS.png
vignettes/BoxPlot_ExprMedpol.png
vignettes/BoxPlot_ExprTukey.png
vignettes/BoxPlot_NormQuant.png
vignettes/BoxPlot_NormSup_BgrdMAS.png
vignettes/BoxPlot_NrmExpMean.png
vignettes/Corrplot_legend.png
vignettes/DensityPlot.png
vignettes/DensityPlotRMA.png
vignettes/DensityPlot_BgrdGC_pm.png
vignettes/DensityPlot_BgrdMAS5_both.png
vignettes/DensityPlot_BgrdRMA.png
vignettes/DensityPlot_DataU133P2.png
vignettes/DensityPlot_ExprDFW.png
vignettes/DensityPlot_ExprFARMS.png
vignettes/DensityPlot_ExprMedpol.png
vignettes/DensityPlot_ExprTukey.png
vignettes/DensityPlot_NormQuant.png
vignettes/DensityPlot_NormSup_BgrdMAS.png
vignettes/DensityPlot_NrmExpMean.png
vignettes/Graph2D.png
vignettes/Graph2DRMA.png
vignettes/Histogram2DRMA.png
vignettes/Histogram2DRMAsurf2.png
vignettes/Histogram3D.png
vignettes/Histogram3DRMA.png
vignettes/Histogram3DRMArotated.png
vignettes/Histogram3Drotated.png
vignettes/HuExon_Diff_XPS_APT_DABG_pval_ps.png
vignettes/HuExon_XPS_APT_MedPol_MvA.png
vignettes/HuExon_XPS_APT_MedPol_MvA_ps.png
vignettes/HuExon_XPS_APT_MedPol_MvA_tc.png
vignettes/HuExon_XPS_APT_RMA_MvA.png
vignettes/HuExon_XPS_APT_RMA_MvA_ps.png
vignettes/HuExon_XPS_APT_RMA_MvA_tc.png
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_ps.png
vignettes/HuExon_XPS_APT_RMA_bg103qu103_MvA_tc.png
vignettes/HuGeneDiff_XPS_APT_DABG_pval_tc_r4.png
vignettes/HuGene_Diff_XPS_APT_DABG_pval.png
vignettes/HuGene_Diff_XPS_DABG_MAS5_pval.png
vignettes/HuGene_XPS_APT_MedPol_MvA.png
vignettes/HuGene_XPS_APT_MedPol_MvA_tc_r4.png
vignettes/HuGene_XPS_APT_RMA_MvA.png
vignettes/HuGene_XPS_APT_RMA_MvA_ps_r4.png
vignettes/HuGene_XPS_APT_RMA_MvA_tc_r4.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_ps_r4.png
vignettes/HuGene_XPS_APT_RMA_bg99qu99_MvA_tc_r4.png
vignettes/Image.png
vignettes/ImageZoom.png
vignettes/Image_BgrdGC_bgrd4.png
vignettes/Image_BgrdMAS4_bgrd4.png
vignettes/Image_BgrdMAS5_8x8_bgrd4.png
vignettes/Image_BgrdMAS5_bgrd4.png
vignettes/Image_BgrdMAS8x8x_bgrd4.png
vignettes/Image_BgrdRMA_bgrd4.png
vignettes/Image_BgrdRMA_data4.png
vignettes/MADplot_legend.png
vignettes/MvAPlot.png
vignettes/ProfileExonRMA.png
vignettes/ScatterPlot_ExprDFW_BrABrB.png
vignettes/ScatterPlot_ExprDFW_BrAPrA.png
vignettes/ScatterPlot_ExprFARMS_BrABrB.png
vignettes/ScatterPlot_ExprFARMS_BrAPrA.png
vignettes/ScatterPlot_ExprMedpol_BrABrB.png
vignettes/ScatterPlot_ExprMedpol_BrAPrA.png
vignettes/ScatterPlot_ExprTukey_BrABrB.png
vignettes/ScatterPlot_ExprTukey_BrAPrA.png
vignettes/ScatterPlot_NormQuant_PM_BrABrB.png
vignettes/ScatterPlot_NormQuant_PM_BrAPrA.png
vignettes/U133P2_APT_PLIER_MvA.png
vignettes/U133P2_APT_PLIER_Scatter.png
vignettes/U133P2_APT_RMA_MvA.png
vignettes/U133P2_APT_RMA_RMAsketch_MvA.png
vignettes/U133P2_Diff_XPS_AFFY_MAS5_pval.png
vignettes/U133P2_XPS_AFFY_APT_RMA.png
vignettes/U133P2_XPS_AFFY_EC_APT_MAS5_pval.png
vignettes/U133P2_XPS_APT_EC_AFFY_MAS5_MvA_3x2.png
vignettes/U133P2_XPS_APT_RMA_MvA.png
vignettes/XPS_APT_HuExon_AdjPValue.png
vignettes/XPS_APT_HuGene_PValue.png
vignettes/XPS_U133P2_Gene_Exon_mean_dot.png
vignettes/XPS_U133P2_HuGene_HuExon_logFC.png
vignettes/xps.Rnw
vignettes/xps.bib
vignettes/xpsClasses.Rnw
vignettes/xpsPreprocess.Rnw
Bioconductor-mirror/xps documentation built on June 1, 2017, 8:13 p.m.