xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Version 1.36.1

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.

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AuthorChristian Stratowa, Vienna, Austria
Bioconductor views DataImport DifferentialExpression ExonArray GeneExpression Microarray OneChannel Preprocessing Transcription
Date of publicationNone
MaintainerChristian Stratowa <cstrato@aon.at>
LicenseGPL (>= 2.0)
Version1.36.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("xps")

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.

Functions

AffyRNAdeg Man page
AnalysisTreeSet Man page
AnalysisTreeSet-class Man page
CELHeader Source code
CELNames Source code
CallTreeSet Man page
CallTreeSet-class Man page
DataTreeSet Man page
DataTreeSet-class Man page
ExprTreeSet Man page
ExprTreeSet-class Man page
Filter-class Man page
FilterTreeSet Man page
FilterTreeSet-class Man page
NUSE Man page
NUSE,QualTreeSet-method Man page
NUSE-methods Man page
PreFilter Man page
PreFilter-class Man page
ProcesSet Man page
ProcesSet-class Man page
ProjectInfo Man page
ProjectInfo-class Man page
QualTreeSet Man page
QualTreeSet-class Man page
RLE Man page
RLE,QualTreeSet-method Man page
RLE-methods Man page
ROOT Man page
SchemeTreeSet Man page
SchemeTreeSet-class Man page
TreeSet Man page
TreeSet-class Man page
UniFilter Man page
UniFilter-class Man page
addData Man page
addData,DataTreeSet-method Man page
addData-methods Man page
adjustXLabMargins Source code
arrayInfo Man page
arrayInfo,ProjectInfo-method Man page
arrayInfo<- Man page
arrayInfo<-,ProjectInfo,character-method Man page
attachBgrd Man page
attachBgrd,DataTreeSet-method Man page
attachBgrd-methods Man page
attachCall Man page
attachCall,CallTreeSet-method Man page
attachCall-methods Man page
attachData Man page
attachData,ProcesSet-method Man page
attachData-methods Man page
attachDataXY Man page
attachDataXY,DataTreeSet-method Man page
attachDataXY-methods Man page
attachExpr Man page
attachExpr,ExprTreeSet-method Man page
attachExpr-methods Man page
attachInten Man page
attachInten,DataTreeSet-method Man page
attachInten-methods Man page
attachMask Man page
attachMask,DataTreeSet-method Man page
attachMask,SchemeTreeSet-method Man page
attachMask-methods Man page
attachPVal Man page
attachPVal,CallTreeSet-method Man page
attachPVal-methods Man page
attachProbe Man page
attachProbe,SchemeTreeSet-method Man page
attachProbe-methods Man page Man page
attachProbeContentGC Man page
attachProbeContentGC,DataTreeSet-method Man page
attachProbeContentGC,SchemeTreeSet-method Man page
attachProbeContentGC-methods Man page
attachProbeSequence Man page
attachProbeSequence,SchemeTreeSet-method Man page
attachUnitNames Man page
attachUnitNames,DataTreeSet-method Man page
attachUnitNames,SchemeTreeSet-method Man page
attachUnitNames-methods Man page
authorInfo Man page
authorInfo,ProjectInfo-method Man page
authorInfo<- Man page
authorInfo<-,ProjectInfo,character-method Man page
background Man page
background,DataTreeSet-method Man page
background<- Man page
background<-,DataTreeSet,data.frame-method Man page
bgcorrect Man page
bgcorrect.gc Man page
bgcorrect.mas4 Man page
bgcorrect.mas5 Man page
bgcorrect.rma Man page
bgtreeNames Man page
bgtreeNames,DataTreeSet-method Man page
biopsyInfo Man page
biopsyInfo,ProjectInfo-method Man page
biopsyInfo<- Man page
biopsyInfo<-,ProjectInfo,character-method Man page
borderplot Man page
borderplot,QualTreeSet-method Man page
borderplot-methods Man page
borders Man page
borders,QualTreeSet-method Man page
boxplot Man page
boxplot,ProcesSet-method Man page
boxplot-methods Man page
callFilter Man page
callFilter,PreFilter-method Man page
callFilter,UniFilter-method Man page
callFilter-methods Man page
callFilter<- Man page
callFilter<-,PreFilter,character-method Man page
callFilter<-,UniFilter,character-method Man page
callTreeset Man page
callTreeset,FilterTreeSet-method Man page
callplot Man page
callplot,CallTreeSet-method Man page
callplot-methods Man page
cellineInfo Man page
cellineInfo,ProjectInfo-method Man page
cellineInfo<- Man page
cellineInfo<-,ProjectInfo,character-method Man page
chipMask Man page
chipMask,SchemeTreeSet-method Man page
chipMask<- Man page
chipMask<-,SchemeTreeSet,data.frame-method Man page
chipName Man page
chipName,ProcesSet-method Man page
chipName,SchemeTreeSet-method Man page
chipProbe Man page
chipProbe,SchemeTreeSet-method Man page
chipProbe<- Man page
chipProbe<-,SchemeTreeSet,data.frame-method Man page
chipType Man page
chipType,ProcesSet-method Man page
chipType,SchemeTreeSet-method Man page
chipType<- Man page
chipType<-,SchemeTreeSet,character-method Man page
coiplot Man page
coiplot,QualTreeSet-method Man page
coiplot-methods Man page
corplot Man page
corplot,ExprTreeSet-method Man page
corplot-methods Man page
cvFilter Man page
cvFilter,PreFilter-method Man page
cvFilter-methods Man page
cvFilter<- Man page
cvFilter<-,PreFilter,numeric-method Man page
dabg.call Man page
datasetInfo Man page
datasetInfo,ProjectInfo-method Man page
datasetInfo<- Man page
datasetInfo<-,ProjectInfo,character-method Man page
debug.xps Man page Source code
dfw Man page
diffFilter Man page
diffFilter,PreFilter-method Man page
diffFilter-methods Man page
diffFilter<- Man page
diffFilter<-,PreFilter,numeric-method Man page
existsROOTFile Man page Source code
exonLevel Man page Source code
exonLevelIDs Source code
export Man page
export,ProcesSet-method Man page
export,SchemeTreeSet-method Man page
export,TreeSet-method Man page
export-methods Man page
export.call Man page
export.data Man page
export.expr Man page
export.filter Man page
export.root Man page
export.scheme Man page
exprTreeset Man page
exprTreeset,FilterTreeSet-method Man page
exprType Man page
exprType,ExprTreeSet-method Man page
exprType<- Man page
exprType<-,ExprTreeSet,character-method Man page
express Man page
exprs Man page
exprs,ExprTreeSet-method Man page
exprs-methods Man page
exprs<- Man page
exprs<-,ExprTreeSet,data.frame-method Man page
extenPart Man page Source code
farms Man page
fcFilter Man page
fcFilter,UniFilter-method Man page
fcFilter-methods Man page
fcFilter<- Man page
fcFilter<-,UniFilter,character-method Man page
fileDir Man page
fileDir,TreeSet-method Man page
fileDir<- Man page
fileDir<-,TreeSet,character-method Man page
filterTreeset Man page
filterTreeset,AnalysisTreeSet-method Man page
firma Man page
firma.expr Man page
firma.score Man page
fitQC Man page
fitRLM Man page
gapFilter Man page
gapFilter,PreFilter-method Man page
gapFilter-methods Man page
gapFilter<- Man page
gapFilter<-,PreFilter,numeric-method Man page
getChipName Man page Source code
getChipType Man page Source code
getDataXY Source code
getDatatype Man page Source code
getNameType Man page Source code
getNumberTrees Man page Source code
getProbeInfo Man page Source code
getTreeData Man page
getTreeData,AnalysisTreeSet-method Man page
getTreeData,FilterTreeSet-method Man page
getTreeData,ProcesSet-method Man page
getTreeData-methods Man page
getTreeNames Man page Source code
highFilter Man page
highFilter,PreFilter-method Man page
highFilter-methods Man page
highFilter<- Man page
highFilter<-,PreFilter,character-method Man page
hist Man page
hist,DataTreeSet-method Man page
hist,ProcesSet-method Man page
hist-methods Man page
hybridizInfo Man page
hybridizInfo,ProjectInfo-method Man page
hybridizInfo<- Man page
hybridizInfo<-,ProjectInfo,character-method Man page
image Man page
image,ProcesSet-method Man page
image,QualTreeSet-method Man page
image-methods Man page
import.data Man page
import.exon.scheme Man page
import.expr.scheme Man page
import.genome.scheme Man page
indexUnits Man page
indexUnits,DataTreeSet-method Man page
indexUnits-methods Man page
ini.call Man page
initialize Man page
initialize,AnalysisTreeSet-method Man page
initialize,CallTreeSet-method Man page
initialize,DataTreeSet-method Man page
initialize,ExprTreeSet-method Man page
initialize,Filter-method Man page
initialize,FilterTreeSet-method Man page
initialize,PreFilter-method Man page
initialize,ProcesSet-method Man page
initialize,ProjectInfo-method Man page
initialize,QualTreeSet-method Man page
initialize,SchemeTreeSet-method Man page
initialize,TreeSet-method Man page
initialize,UniFilter-method Man page
initialize-methods Man page
intensity Man page
intensity,DataTreeSet-method Man page
intensity-methods Man page
intensity2GCplot Man page
intensity2GCplot,DataTreeSet-method Man page
intensity2GCplot-methods Man page
intensity<- Man page
intensity<-,DataTreeSet,data.frame-method Man page
isChipType Source code
isFilterCondition Source code
isROOTFile Man page Source code
lowFilter Man page
lowFilter,PreFilter-method Man page
lowFilter-methods Man page
lowFilter<- Man page
lowFilter<-,PreFilter,character-method Man page
madFilter Man page
madFilter,PreFilter-method Man page
madFilter-methods Man page
madFilter<- Man page
madFilter<-,PreFilter,numeric-method Man page
madplot Man page
madplot,ExprTreeSet-method Man page
madplot-methods Man page
mas4 Man page
mas5 Man page
mas5.call Man page
mboxplot Man page
mboxplot,ProcesSet-method Man page
mboxplot-methods Man page
metaProbesets Man page Source code
mm Man page
mm,DataTreeSet-method Man page
mm-methods Man page
mmindex Man page
mmindex,DataTreeSet-method Man page
mmindex-methods Man page
mvaplot Man page
mvaplot,ExprTreeSet-method Man page
mvaplot-methods Man page
namePart Man page Source code
ncols Man page
ncols,DataTreeSet-method Man page
ncols,SchemeTreeSet-method Man page
normType Man page
normType,ExprTreeSet-method Man page
normType<- Man page
normType<-,ExprTreeSet,character-method Man page
normalize Man page
normalize.constant Man page
normalize.lowess Man page
normalize.quantiles Man page
normalize.supsmu Man page
nrows Man page
nrows,DataTreeSet-method Man page
nrows,SchemeTreeSet-method Man page
numberFilters Man page
numberFilters,Filter-method Man page
nuseplot Man page
nuseplot,ExprTreeSet-method Man page
nuseplot,QualTreeSet-method Man page
nuseplot-methods Man page
onAttach Source code
onUnload Source code
pcaplot Man page
pcaplot,ExprTreeSet-method Man page
pcaplot-methods Man page
plotAffyRNAdeg Man page
plotBorder Man page
plotBoxplot Man page
plotCOI Man page
plotCall Man page
plotCorr Man page
plotDensities Source code
plotDensity Man page
plotImage Man page
plotIntensity2GC Man page
plotMA Man page
plotMAD Man page
plotNUSE Man page
plotPCA Man page
plotPM Man page
plotProbeset Man page
plotRLE Man page
plotVolcano Man page
pm Man page
pm,DataTreeSet-method Man page
pm-methods Man page
pmindex Man page
pmindex,DataTreeSet-method Man page
pmindex-methods Man page
pmplot Man page
pmplot,DataTreeSet-method Man page
pmplot-methods Man page
prefilter Man page
presCall Man page
presCall,CallTreeSet-method Man page
presCall-methods Man page
presCall<- Man page
presCall<-,CallTreeSet,data.frame-method Man page
primcellInfo Man page
primcellInfo,ProjectInfo-method Man page
primcellInfo<- Man page
primcellInfo<-,ProjectInfo,character-method Man page
probeContentGC Man page
probeContentGC,SchemeTreeSet-method Man page
probeContentGC-methods Man page
probeInfo Man page
probeInfo,SchemeTreeSet-method Man page
probeSequence Man page
probeSequence,SchemeTreeSet-method Man page
probeSequence-methods Man page
probesetID2unitID Man page
probesetID2unitID,DataTreeSet-method Man page
probesetID2unitID,SchemeTreeSet-method Man page
probesetID2unitID-methods Man page
probesetplot Man page
probesetplot,DataTreeSet-method Man page
probesetplot-methods Man page
projectInfo Man page
projectInfo,DataTreeSet-method Man page
projectInfo,ProjectInfo-method Man page
projectInfo<- Man page
projectInfo<-,DataTreeSet,ProjectInfo-method Man page
projectInfo<-,ProjectInfo,character-method Man page
pseudoPalette Source code
pvalData Man page
pvalData,CallTreeSet-method Man page
pvalData-methods Man page
pvalData<- Man page
pvalData<-,CallTreeSet,data.frame-method Man page
qualOption Man page
qualOption,QualTreeSet-method Man page
qualOption<- Man page
qualOption<-,QualTreeSet,character-method Man page
qualType Man page
qualType,QualTreeSet-method Man page
qualType<- Man page
qualType<-,QualTreeSet,character-method Man page
qualify Man page
qualify.rlm Man page
quantileFilter Man page
quantileFilter,PreFilter-method Man page
quantileFilter-methods Man page
quantileFilter<- Man page
quantileFilter<-,PreFilter,numeric-method Man page
ratioFilter Man page
ratioFilter,PreFilter-method Man page
ratioFilter-methods Man page
ratioFilter<- Man page
ratioFilter<-,PreFilter,numeric-method Man page
rawCELName Man page
rawCELName,DataTreeSet-method Man page
rawCELName-methods Man page
removeBgrd Man page
removeBgrd,DataTreeSet-method Man page
removeBgrd-methods Man page
removeCall Man page
removeCall,CallTreeSet-method Man page
removeCall-methods Man page
removeData Man page
removeData,ProcesSet-method Man page
removeData-methods Man page
removeDataXY Man page
removeDataXY,DataTreeSet-method Man page
removeDataXY-methods Man page
removeExpr Man page
removeExpr,ExprTreeSet-method Man page
removeExpr-methods Man page
removeInten Man page
removeInten,DataTreeSet-method Man page
removeInten-methods Man page
removeMask Man page
removeMask,DataTreeSet-method Man page
removeMask,SchemeTreeSet-method Man page
removeMask-methods Man page
removePVal Man page
removePVal,CallTreeSet-method Man page
removePVal-methods Man page
removeProbe Man page
removeProbe,SchemeTreeSet-method Man page
removeProbeContentGC Man page
removeProbeContentGC,DataTreeSet-method Man page
removeProbeContentGC,SchemeTreeSet-method Man page
removeProbeContentGC-methods Man page
removeProbeSequence Man page
removeProbeSequence,SchemeTreeSet-method Man page
removeProbeSequence-methods Man page Man page
removeUnitNames Man page
removeUnitNames,DataTreeSet-method Man page
removeUnitNames,SchemeTreeSet-method Man page
removeUnitNames-methods Man page
residuals Man page
residuals,QualTreeSet-method Man page
rleplot Man page
rleplot,ExprTreeSet-method Man page
rleplot,QualTreeSet-method Man page
rleplot-methods Man page
rma Man page
rmaPLM Man page
root.browser Man page
root.browser,TreeSet-method Man page
root.call Man page
root.data Man page
root.density Man page
root.expr Man page
root.graph1D Man page
root.graph2D Man page
root.hist1D Man page
root.hist2D Man page
root.hist3D Man page
root.image Man page
root.merge.data Man page
root.mvaplot Man page
root.profile Man page
root.scheme Man page
rootDirFile Source code
rootDrawName Source code
rootFile Man page
rootFile,TreeSet-method Man page
rootFile<- Man page
rootFile<-,TreeSet,character-method Man page
sampleInfo Man page
sampleInfo,ProjectInfo-method Man page
sampleInfo<- Man page
sampleInfo<-,ProjectInfo,character-method Man page
schemeFile Man page
schemeFile,ProcesSet-method Man page
schemeFile<- Man page
schemeFile<-,ProcesSet,character-method Man page
schemeSet Man page
schemeSet,ProcesSet-method Man page
schemeSet<- Man page
schemeSet<-,ProcesSet,SchemeTreeSet-method Man page
se.exprs Man page
se.exprs,ExprTreeSet-method Man page
setName Man page
setName,TreeSet-method Man page
setName<- Man page
setName<-,TreeSet,character-method Man page
setType Man page
setType,TreeSet-method Man page
setType<- Man page
setType<-,TreeSet,character-method Man page
show,ProjectInfo-method Man page
sourceInfo Man page
sourceInfo,ProjectInfo-method Man page
sourceInfo<- Man page
sourceInfo<-,ProjectInfo,character-method Man page
summarize Man page
summarize.mas4 Man page
summarize.mas5 Man page
summarize.rma Man page
summaryAffyRNAdeg Man page
symbol2unitID Man page
symbol2unitID,DataTreeSet-method Man page
symbol2unitID,SchemeTreeSet-method Man page
symbol2unitID-methods Man page
tissueInfo Man page
tissueInfo,ProjectInfo-method Man page
tissueInfo<- Man page
tissueInfo<-,ProjectInfo,character-method Man page
transcriptID2unitID Man page
transcriptID2unitID,DataTreeSet-method Man page
transcriptID2unitID,SchemeTreeSet-method Man page
transcriptID2unitID-methods Man page
treatmentInfo Man page
treatmentInfo,ProjectInfo-method Man page
treatmentInfo<- Man page
treatmentInfo<-,ProjectInfo,character-method Man page
treeData Man page
treeData,ProcesSet-method Man page
treeInfo Man page
treeInfo,TreeSet-method Man page
treeInfo-methods Man page
treeNames Man page
treeNames,TreeSet-method Man page
trma Man page
type2Exten Man page Source code
uniTest Man page
uniTest,UniFilter-method Man page
uniTest-methods Man page
uniTest<- Man page
uniTest<-,UniFilter,character-method Man page
unifilter Man page
unitID2probesetID Man page
unitID2probesetID,DataTreeSet-method Man page
unitID2probesetID,SchemeTreeSet-method Man page
unitID2probesetID-methods Man page
unitID2symbol Man page
unitID2symbol,DataTreeSet-method Man page
unitID2symbol,SchemeTreeSet-method Man page
unitID2symbol-methods Man page
unitID2transcriptID Man page
unitID2transcriptID,DataTreeSet-method Man page
unitID2transcriptID,SchemeTreeSet-method Man page
unitID2transcriptID-methods Man page
unitNames Man page
unitNames,SchemeTreeSet-method Man page
unitNames<- Man page
unitNames<-,SchemeTreeSet,data.frame-method Man page
unitestFilter Man page
unitestFilter,UniFilter-method Man page
unitestFilter-methods Man page
unitestFilter<- Man page
unitestFilter<-,UniFilter,character-method Man page
validBgrd Man page
validBgrd,DataTreeSet-method Man page
validCall Man page
validCall,CallTreeSet-method Man page
validData Man page
validData,AnalysisTreeSet-method Man page
validData,DataTreeSet-method Man page
validData,FilterTreeSet-method Man page
validData,ProcesSet-method Man page
validEstimatorOption Source code
validExpr Man page
validExpr,ExprTreeSet-method Man page
validFilter Man page
validFilter,AnalysisTreeSet-method Man page
validLogbase Source code
validMsg Source code
validOption Source code
validOutfile Source code
validPVal Man page
validPVal,CallTreeSet-method Man page
validQualityOption Source code
validROOTFile Source code
validSE Man page
validSE,ExprTreeSet-method Man page
validSchemeTreeSet Source code
validSeparator Source code
validTempDir Source code
validTranscriptOption Source code
validTreenames Source code
validTreetype Man page Source code
varFilter Man page
varFilter,PreFilter-method Man page
varFilter-methods Man page
varFilter<- Man page
varFilter<-,PreFilter,numeric-method Man page
volcanoplot Man page
volcanoplot,AnalysisTreeSet-method Man page
volcanoplot-methods Man page
weights Man page
weights,QualTreeSet-method Man page
xps Man page
xps-package Man page
xpsBgCorrect Man page
xpsBgCorrect,DataTreeSet-method Man page
xpsBgCorrect-methods Man page
xpsDABGCall Man page
xpsDABGCall,DataTreeSet-method Man page
xpsDABGCall-methods Man page
xpsFIRMA Man page
xpsFIRMA,DataTreeSet-method Man page
xpsFIRMA-methods Man page
xpsINICall Man page
xpsINICall,DataTreeSet-method Man page
xpsINICall-methods Man page
xpsMAS4 Man page
xpsMAS4,DataTreeSet-method Man page
xpsMAS4-methods Man page
xpsMAS5 Man page
xpsMAS5,DataTreeSet-method Man page
xpsMAS5-methods Man page
xpsMAS5Call Man page
xpsMAS5Call,DataTreeSet-method Man page
xpsMAS5Call-methods Man page
xpsNormalize Man page
xpsNormalize,DataTreeSet-method Man page
xpsNormalize,ExprTreeSet-method Man page
xpsNormalize-methods Man page
xpsOptions Man page Source code
xpsPreFilter Man page
xpsPreFilter,ExprTreeSet-method Man page
xpsPreFilter-methods Man page
xpsPreprocess Man page
xpsPreprocess,DataTreeSet-method Man page
xpsPreprocess-methods Man page
xpsQAReport Man page Source code
xpsQualify Man page
xpsQualify,DataTreeSet-method Man page
xpsQualify-methods Man page
xpsQualityControl Man page
xpsQualityControl,DataTreeSet-method Man page
xpsQualityControl-methods Man page
xpsRMA Man page
xpsRMA,DataTreeSet-method Man page
xpsRMA-methods Man page
xpsRNAdeg Man page
xpsRNAdeg,QualTreeSet-method Man page
xpsRNAdeg-methods Man page
xpsSummarize Man page
xpsSummarize,DataTreeSet-method Man page
xpsSummarize-methods Man page
xpsUniFilter Man page
xpsUniFilter,ExprTreeSet-method Man page
xpsUniFilter-methods Man page

Files

.BBSoptions
ACKNOWLEDGMENT
DESCRIPTION
INSTALL
NAMESPACE
NEWS
R
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
build
build/vignette.rds
configure
configure.in
configure.vc10.win
configure.win
findroot.pl
findvc.pl
inst
inst/ACKNOWLEDGMENT
inst/CHANGELOG
inst/INSTALL
inst/QC
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/doc
inst/doc/APTvsXPS.R
inst/doc/APTvsXPS.Rnw
inst/doc/APTvsXPS.pdf
inst/doc/xps.R
inst/doc/xps.Rnw
inst/doc/xps.pdf
inst/doc/xpsClasses.R
inst/doc/xpsClasses.Rnw
inst/doc/xpsClasses.pdf
inst/doc/xpsPreprocess.R
inst/doc/xpsPreprocess.Rnw
inst/doc/xpsPreprocess.pdf
inst/examples
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
inst/raw/TestA1.CEL
inst/raw/TestA2.CEL
inst/raw/TestB1.CEL
inst/raw/TestB2.CEL
inst/rootdata
inst/rootdata/DataTest3_cel.root
inst/rootdata/tmp_Test3RMA.root
inst/rootsrc
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
inst/schemes/SchemeTest3.root
man
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
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
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
xps documentation built on May 20, 2017, 10:19 p.m.