Man pages for xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

addData-methodsImport additional CEL files into a DataTreeSet
AffyRNAdegFunctions to assess RNA Degradation.
AnalysisTreeSet-classClass AnalysisTreeSet
attachBgrd-methodsAttach/Remove Background Intensities
attachCall-methodsAttach/Remove Detecion Call Measures
attachData-methodsAttach/Remove Data
attachDataXY-methodsAttach/Remove (X,Y)-Coordinates
attachExpr-methodsAttach/Remove Expression Measures
attachInten-methodsAttach/Remove Intensities
attachMask-methodsAttach/Remove Scheme Mask
attachProbe-methodsAttach/Remove Probe Sequence and/or GC Content
attachUnitNames-methodsAttach/Remove Unit Names
bgcorrectBackground Correction
borderplot-methodsPlots of Border Elements
boxplot-methodsBox Plots
callFilter-methodsDetection Call Filter
callplot-methodsBarplot of Percent Present and Absent Calls.
CallTreeSet-classClass CallTreeSet
coiplot-methodsCenter-Of-Intensity QC Plots
corplot-methodsArray-Array Expression Level Correlation Plot
cvFilter-methodsCoefficient of Variation Filter
dabg.callDetection Above Background Call
DataTreeSet-classClass DataTreeSet
dfwDistribution Free Weighted Expression Measure
diffFilter-methodsDifference Filter
existsROOTFileTest for Existing ROOT File
exonLevelConversion of Parameter exonlevel to Integer
exportExport data as text files
export.filterExport filter data as text files
export.rootExport data from ROOT file
expressCompute expression levels from raw data
exprs-methodsGet/Set Expression Values
ExprTreeSet-classClass ExprTreeSet
extenPartGet Extension of Tree Names
farmsFactor Analysis for Robust Microarray Summarization...
fcFilter-methodsFold-Change Filter
Filter-classBase Class Filter
FilterTreeSet-classClass FilterTreeSet
firmaFinding Isoforms using Robust Multichip Analysis
firma.exprGet Expression Levels from FIRMA
firma.scoreGet Splice Score from FIRMA
fitQCFunctions for fitting probe-level models
fitRLMFunctions for fitting RMA as probe-level model
gapFilter-methodsGap Filter
getChipNameGet Chip Name
getChipTypeGet Chip Type
getDatatypeGet Data Type
getNameTypeGet Chip Name and Type
getNumberTreesGet Number of Trees
getProbeInfoGet Probe Information
getTreeData-methodsExport Tree Data
getTreeNamesGet Tree Names
highFilter-methodsUpper Threshold Filter
hist-methodsPlot Density Estimate
image-methodsDisplay an Image
import.dataImport CEL files into a DataTreeSet
import.exon.schemeImport CLF, PGF and annotation files into a SchemeTreeSet
import.expr.schemeImport CDF, probe and annotation files into a SchemeTreeSet
import.genome.schemeImport CLF, PGF and annotation files into a SchemeTreeSet
indexUnits-methodsUnit Locations
ini.callInformative/Non-Informative Call
initialize-methodsInitialize Classes
intensity2GCplot-methodsBoxlot of Probe Intensities Stratified by GC Content.
intensity-methodsGet/Set Data Values
isROOTFileTest for ROOT File
lowFilter-methodsLower Threshold Filter
madFilter-methodsMedian Absolute Deviation Filter
madplot-methodsArray-Array Expression Level Distance Plot
mas4MAS 4.0 Expression Measure
mas5MAS 5.0 Expression Measure
mas5.callMAS 5.0 Absolute Detection Call
mboxplot-methodsBox Plots of Relative M Values
metaProbesetsCreate MetaProbeset File for APT
mvaplot-methodsM vs A Plot
namePartGet Tree Names w/o Extension
normalizeNormalization on Affymetrix Probe Level Data or on Expression...
NUSENormalized Unscaled Standard Errors (NUSE)
nuseplot-methodsBox Plots of Normalized Unscaled Standard Errors (NUSE)
pcaplot-methodsPCA Plot
plotBorderPlots of Border Elements for Device
plotBoxplotBox Plots for Device
plotCallBarplot of Percent Present and Absent Calls for Device
plotCOICenter-Of-Intensity QC Plots for Device
plotCorrArray-Array Expression Level Correlation Plot for Device
plotDensityPlot Density Estimate for Device
plotImagePlot Image(s) for Device
plotIntensity2GCBoxlot of Probe Intensities Stratified by GC Content for...
plotMAMvA Scatter Plot for Device
plotMADArray-Array Expression Level Distance Plot for Device
plotNUSEBox Plots of Normalized Unscaled Standard Errors (NUSE) for...
plotPCAPCA Plot for Device
plotPMBarplot of PM and MM Intensities for Device
plotProbesetPlot of Probe Intensities for a Probeset for Device.
plotRLEBox Plots of Relative Log Expression (RLE) for Device
plotVolcanoVolcano Plot
pm-methodsMethods for accessing perfect matches and mismatches
pmplot-methodsBarplot of PM and MM Intensities.
prefilterFunction for Applying a PreFilter to an ExprTreeSet
PreFilter-classClass PreFilter
PreFilter-constructorConstructor for Class PreFilter
presCall-methodsGet/Set Present Call Values
probeContentGC-methodsGet G/C Content for Probes
probeSequence-methodsGet Probe Sequence
probesetID2unitID-methodsConversion between Probeset IDs and UnitIDs
probesetplot-methodsPlot of Probe Intensities for a Probeset.
ProcesSet-classClass ProcesSet
ProjectInfo-classClass ProjectInfo
ProjectInfo-constructorConstructor for Class ProjectInfo
qualifyProbe Set Quality Control Functions
QualTreeSet-classClass QualTreeSet
quantileFilter-methodsQuantile Filter
ratioFilter-methodsRatio Filter
rawCELName-methodsMethod for getting names of the raw CEL-files
RLERelative Log Expression (RLE)
rleplot-methodsBox Plots of Relative Log Expression (RLE)
rmaRobust Multi-Array Average Expression Measure
ROOTROOT An Object-Oriented Data Analysis Framework
root.browser-methodsOpen the ROOT object browser
root.callCreate class CallTreeSet accessing ROOT detection call file
root.dataCreate class DataTreeSet accessing ROOT data file
root.densityROOT Density Plot
root.exprCreate class ExprTreeSet accessing ROOT expression file
root.graph1DROOT 1D-Graph
root.graph2DROOT 2D-Graph
root.hist1DROOT 1D-Histogram
root.hist2DROOT 2D-Histogram
root.hist3DROOT 3D-Histogram
root.imageROOT Image
root.merge.dataCreate class DataTreeSet by merging ROOT data files
root.mvaplotROOT M vs A Plot
root.profileROOT Profile Plot
root.schemeCreate class SchemeTreeSet accessing ROOT scheme file
SchemeTreeSet-classClass SchemeTreeSet
summarizeProbe Set Summarizing Functions
symbol2unitID-methodsConversion between Gene Symbols and UnitIDs
treeInfo-methodsGet UserInfo from ROOT Trees
TreeSet-classClass TreeSet
trmatransposed Robust Multi-Array Average Expression Measure
type2ExtenConvert Method Type to Tree Extension
unifilterFunction for Applying an UniFilter to an ExprTreeSet
UniFilter-classClass UniFilter
UniFilter-constructorConstructor for Class UniFilter
unitestFilter-methodsUnitest Filter
uniTest-methodsA Two-Group Unitest
validCall-methodsGet Valid Detection Call Values
validData-methodsExtract Subset of Data
validExpr-methodsGet Valid Expression Levels
validSE-methodsGet Valid Standard Errors
validTreetypeValidate Tree Type
varFilter-methodsVariance Filter
volcanoplot-methodsVolcano Plot
xpsOptionsxps Options
xps-packagexps Package Overview
xpsQAReportCreate Quality Assessment Report.
xps documentation built on Nov. 1, 2018, 2:29 a.m.