# Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

## Documentation for package ‘xps’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P Q R S T U V W X

xps-package | xps Package Overview

## -- A --

addData | Import additional CEL files into a DataTreeSet
addData-method | Class DataTreeSet
addData-methods | Import additional CEL files into a DataTreeSet
AffyRNAdeg | Functions to assess RNA Degradation.
AnalysisTreeSet | Class AnalysisTreeSet
AnalysisTreeSet-class | Class AnalysisTreeSet
arrayInfo | Class ProjectInfo
arrayInfo-method | Class ProjectInfo
arrayInfo<- | Class ProjectInfo
arrayInfo<--method | Class ProjectInfo
attachBgrd | Attach/Remove Background Intensities
attachBgrd-method | Class DataTreeSet
attachBgrd-methods | Attach/Remove Background Intensities
attachCall | Attach/Remove Detecion Call Measures
attachCall-method | Class CallTreeSet
attachCall-methods | Attach/Remove Detecion Call Measures
attachData | Attach/Remove Data
attachData-method | Class ProcesSet
attachData-methods | Attach/Remove Data
attachDataXY | Attach/Remove (X,Y)-Coordinates
attachDataXY-method | Class DataTreeSet
attachDataXY-methods | Attach/Remove (X,Y)-Coordinates
attachExpr | Attach/Remove Expression Measures
attachExpr-method | Class ExprTreeSet
attachExpr-methods | Attach/Remove Expression Measures
attachInten | Attach/Remove Intensities
attachInten-method | Class DataTreeSet
attachInten-methods | Attach/Remove Intensities
attachMask | Attach/Remove Scheme Mask
attachMask-method | Class DataTreeSet
attachMask-method | Class SchemeTreeSet
attachMask-methods | Attach/Remove Scheme Mask
attachProbe | Attach/Remove Probe Sequence and/or GC Content
attachProbe-method | Class SchemeTreeSet
attachProbe-methods | Attach/Remove Probe Sequence and/or GC Content
attachProbeContentGC | Attach/Remove Probe Sequence and/or GC Content
attachProbeContentGC-method | Class DataTreeSet
attachProbeContentGC-method | Class SchemeTreeSet
attachProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content
attachProbeSequence | Attach/Remove Probe Sequence and/or GC Content
attachProbeSequence-method | Class SchemeTreeSet
attachPVal | Attach/Remove Detecion Call Measures
attachPVal-method | Class CallTreeSet
attachPVal-methods | Attach/Remove Detecion Call Measures
attachUnitNames | Attach/Remove Unit Names
attachUnitNames-method | Class DataTreeSet
attachUnitNames-method | Class SchemeTreeSet
attachUnitNames-methods | Attach/Remove Unit Names
authorInfo | Class ProjectInfo
authorInfo-method | Class ProjectInfo
authorInfo<- | Class ProjectInfo
authorInfo<--method | Class ProjectInfo

## -- B --

background | Class DataTreeSet
background-method | Class DataTreeSet
background<- | Class DataTreeSet
background<--method | Class DataTreeSet
bgcorrect | Background Correction
bgcorrect.gc | Background Correction
bgcorrect.mas4 | Background Correction
bgcorrect.mas5 | Background Correction
bgcorrect.rma | Background Correction
bgtreeNames | Class DataTreeSet
bgtreeNames-method | Class DataTreeSet
biopsyInfo | Class ProjectInfo
biopsyInfo-method | Class ProjectInfo
biopsyInfo<- | Class ProjectInfo
biopsyInfo<--method | Class ProjectInfo
borderplot | Plots of Border Elements
borderplot-method | Class QualTreeSet
borderplot-methods | Plots of Border Elements
borders | Class QualTreeSet
borders-method | Class QualTreeSet
boxplot | Box Plots
boxplot-method | Class ProcesSet
boxplot-methods | Box Plots

## -- C --

callFilter | Detection Call Filter
callFilter-method | Class PreFilter
callFilter-method | Class UniFilter
callFilter-methods | Detection Call Filter
callFilter<- | Detection Call Filter
callFilter<--method | Class PreFilter
callFilter<--method | Class UniFilter
callplot | Barplot of Percent Present and Absent Calls.
callplot-method | Class CallTreeSet
callplot-methods | Barplot of Percent Present and Absent Calls.
CallTreeSet | Class CallTreeSet
callTreeset | Class FilterTreeSet
CallTreeSet-class | Class CallTreeSet
callTreeset-method | Class FilterTreeSet
cellineInfo | Class ProjectInfo
cellineInfo-method | Class ProjectInfo
cellineInfo<- | Class ProjectInfo
cellineInfo<--method | Class ProjectInfo
chipMask | Class SchemeTreeSet
chipMask-method | Class SchemeTreeSet
chipMask<- | Class SchemeTreeSet
chipMask<--method | Class SchemeTreeSet
chipName | Class SchemeTreeSet
chipName-method | Class ProcesSet
chipName-method | Class SchemeTreeSet
chipProbe | Class SchemeTreeSet
chipProbe-method | Class SchemeTreeSet
chipProbe<- | Class SchemeTreeSet
chipProbe<--method | Class SchemeTreeSet
chipType | Class SchemeTreeSet
chipType-method | Class ProcesSet
chipType-method | Class SchemeTreeSet
chipType<- | Class SchemeTreeSet
chipType<--method | Class SchemeTreeSet
coiplot | Center-Of-Intensity QC Plots
coiplot-method | Class QualTreeSet
coiplot-methods | Center-Of-Intensity QC Plots
corplot | Array-Array Expression Level Correlation Plot
corplot-method | Class ExprTreeSet
corplot-methods | Array-Array Expression Level Correlation Plot
cvFilter | Coefficient of Variation Filter
cvFilter-method | Class PreFilter
cvFilter-methods | Coefficient of Variation Filter
cvFilter<- | Coefficient of Variation Filter
cvFilter<--method | Class PreFilter

## -- D --

dabg.call | Detection Above Background Call
datasetInfo | Class ProjectInfo
datasetInfo-method | Class ProjectInfo
datasetInfo<- | Class ProjectInfo
datasetInfo<--method | Class ProjectInfo
DataTreeSet | Class DataTreeSet
DataTreeSet-class | Class DataTreeSet
debug.xps | xps Options
dfw | Distribution Free Weighted Expression Measure
diffFilter | Difference Filter
diffFilter-method | Class PreFilter
diffFilter-methods | Difference Filter
diffFilter<- | Difference Filter
diffFilter<--method | Class PreFilter

## -- E --

existsROOTFile | Test for Existing ROOT File
exonLevel | Conversion of Parameter exonlevel to Integer
export | Export data as text files
export-method | Class ProcesSet
export-method | Class SchemeTreeSet
export-method | Class TreeSet
export-methods | Export data as text files
export.call | Export data as text files
export.data | Export data as text files
export.expr | Export data as text files
export.filter | Export filter data as text files
export.root | Export data from ROOT file
export.scheme | Export data as text files
express | Compute expression levels from raw data
exprs | Get/Set Expression Values
exprs-method | Class ExprTreeSet
exprs-methods | Get/Set Expression Values
exprs<- | Get/Set Expression Values
exprs<--method | Class ExprTreeSet
ExprTreeSet | Class ExprTreeSet
exprTreeset | Class FilterTreeSet
ExprTreeSet-class | Class ExprTreeSet
exprTreeset-method | Class FilterTreeSet
exprType | Class ExprTreeSet
exprType-method | Class ExprTreeSet
exprType<- | Class ExprTreeSet
exprType<--method | Class ExprTreeSet
extenPart | Get Extension of Tree Names

## -- F --

farms | Factor Analysis for Robust Microarray Summarization Expression Measure
fcFilter | Fold-Change Filter
fcFilter-method | Class UniFilter
fcFilter-methods | Fold-Change Filter
fcFilter<- | Fold-Change Filter
fcFilter<--method | Class UniFilter
fileDir | Class TreeSet
fileDir-method | Class TreeSet
fileDir<- | Class TreeSet
fileDir<--method | Class TreeSet
Filter-class | Base Class Filter
FilterTreeSet | Class FilterTreeSet
filterTreeset | Class AnalysisTreeSet
FilterTreeSet-class | Class FilterTreeSet
filterTreeset-method | Class AnalysisTreeSet
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

## -- G --

gapFilter | Gap Filter
gapFilter-method | Class PreFilter
gapFilter-methods | Gap Filter
gapFilter<- | Gap Filter
gapFilter<--method | Class PreFilter
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 | Export Tree Data
getTreeData-method | Class AnalysisTreeSet
getTreeData-method | Class FilterTreeSet
getTreeData-method | Class ProcesSet
getTreeData-methods | Export Tree Data
getTreeNames | Get Tree Names

## -- H --

highFilter | Upper Threshold Filter
highFilter-method | Class PreFilter
highFilter-methods | Upper Threshold Filter
highFilter<- | Upper Threshold Filter
highFilter<--method | Class PreFilter
hist | Plot Density Estimate
hist-method | Class DataTreeSet
hist-method | Class ProcesSet
hist-methods | Plot Density Estimate
hybridizInfo | Class ProjectInfo
hybridizInfo-method | Class ProjectInfo
hybridizInfo<- | Class ProjectInfo
hybridizInfo<--method | Class ProjectInfo

## -- I --

image | Display an Image
image-method | Class ProcesSet
image-method | Class QualTreeSet
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 | Unit Locations
indexUnits-method | Class DataTreeSet
indexUnits-methods | Unit Locations
ini.call | Informative/Non-Informative Call
initialize | Initialize Classes
initialize-method | Initialize Classes
initialize-methods | Initialize Classes
intensity | Get/Set Data Values
intensity-method | Class DataTreeSet
intensity-methods | Get/Set Data Values
intensity2GCplot | Boxlot of Probe Intensities Stratified by GC Content.
intensity2GCplot-method | Class DataTreeSet
intensity2GCplot-methods | Boxlot of Probe Intensities Stratified by GC Content.
intensity<- | Get/Set Data Values
intensity<--method | Class DataTreeSet
isROOTFile | Test for ROOT File

## -- L --

lowFilter | Lower Threshold Filter
lowFilter-method | Class PreFilter
lowFilter-methods | Lower Threshold Filter
lowFilter<- | Lower Threshold Filter
lowFilter<--method | Class PreFilter

## -- M --

madFilter | Median Absolute Deviation Filter
madFilter-method | Class PreFilter
madFilter-methods | Median Absolute Deviation Filter
madFilter<- | Median Absolute Deviation Filter
madFilter<--method | Class PreFilter
madplot | Array-Array Expression Level Distance Plot
madplot-method | Class ExprTreeSet
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 | Box Plots of Relative M Values
mboxplot-method | Class ProcesSet
mboxplot-methods | Box Plots of Relative M Values
metaProbesets | Create MetaProbeset File for APT
mm | Methods for accessing perfect matches and mismatches
mm-method | Class DataTreeSet
mm-methods | Methods for accessing perfect matches and mismatches
mmindex | Unit Locations
mmindex-method | Class DataTreeSet
mmindex-methods | Unit Locations
mvaplot | M vs A Plot
mvaplot-method | Class ExprTreeSet
mvaplot-methods | M vs A Plot

## -- N --

namePart | Get Tree Names w/o Extension
ncols | Class SchemeTreeSet
ncols-method | Class DataTreeSet
ncols-method | Class SchemeTreeSet
normalize | Normalization on Affymetrix Probe Level Data or on Expression Levels
normalize.constant | Normalization on Affymetrix Probe Level Data or on Expression Levels
normalize.lowess | Normalization on Affymetrix Probe Level Data or on Expression Levels
normalize.quantiles | Normalization on Affymetrix Probe Level Data or on Expression Levels
normalize.supsmu | Normalization on Affymetrix Probe Level Data or on Expression Levels
normType | Class ExprTreeSet
normType-method | Class ExprTreeSet
normType<- | Class ExprTreeSet
normType<--method | Class ExprTreeSet
nrows | Class SchemeTreeSet
nrows-method | Class DataTreeSet
nrows-method | Class SchemeTreeSet
numberFilters | Base Class Filter
numberFilters-method | Base Class Filter
NUSE | Normalized Unscaled Standard Errors (NUSE)
NUSE-method | Class QualTreeSet
NUSE-methods | Normalized Unscaled Standard Errors (NUSE)
nuseplot | Box Plots of Normalized Unscaled Standard Errors (NUSE)
nuseplot-method | Class ExprTreeSet
nuseplot-method | Class QualTreeSet
nuseplot-methods | Box Plots of Normalized Unscaled Standard Errors (NUSE)

## -- P --

pcaplot | PCA Plot
pcaplot-method | Class ExprTreeSet
pcaplot-methods | PCA Plot
plotAffyRNAdeg | Functions to assess RNA Degradation.
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 Device.
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 Device
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 for accessing perfect matches and mismatches
pm-method | Class DataTreeSet
pm-methods | Methods for accessing perfect matches and mismatches
pmindex | Unit Locations
pmindex-method | Class DataTreeSet
pmindex-methods | Unit Locations
pmplot | Barplot of PM and MM Intensities.
pmplot-method | Class DataTreeSet
pmplot-methods | Barplot of PM and MM Intensities.
PreFilter | Constructor for Class PreFilter
prefilter | Function for Applying a PreFilter to an ExprTreeSet
PreFilter-class | Class PreFilter
presCall | Get/Set Present Call Values
presCall-method | Class CallTreeSet
presCall-methods | Get/Set Present Call Values
presCall<- | Get/Set Present Call Values
presCall<--method | Class CallTreeSet
primcellInfo | Class ProjectInfo
primcellInfo-method | Class ProjectInfo
primcellInfo<- | Class ProjectInfo
primcellInfo<--method | Class ProjectInfo
probeContentGC | Get G/C Content for Probes
probeContentGC-method | Class SchemeTreeSet
probeContentGC-methods | Get G/C Content for Probes
probeInfo | Class SchemeTreeSet
probeInfo-method | Class SchemeTreeSet
probeSequence | Get Probe Sequence
probeSequence-method | Class SchemeTreeSet
probeSequence-methods | Get Probe Sequence
probesetID2unitID | Conversion between Probeset IDs and UnitIDs
probesetID2unitID-method | Class DataTreeSet
probesetID2unitID-method | Class SchemeTreeSet
probesetID2unitID-methods | Conversion between Probeset IDs and UnitIDs
probesetplot | Plot of Probe Intensities for a Probeset.
probesetplot-method | Class DataTreeSet
probesetplot-methods | Plot of Probe Intensities for a Probeset.
ProcesSet | Class ProcesSet
ProcesSet-class | Class ProcesSet
ProjectInfo | Constructor for Class ProjectInfo
projectInfo | Class ProjectInfo
ProjectInfo-class | Class ProjectInfo
projectInfo-method | Class DataTreeSet
projectInfo-method | Class ProjectInfo
projectInfo<- | Class ProjectInfo
projectInfo<--method | Class DataTreeSet
projectInfo<--method | Class ProjectInfo
pvalData | Get/Set Present Call Values
pvalData-method | Class CallTreeSet
pvalData-methods | Get/Set Present Call Values
pvalData<- | Get/Set Present Call Values
pvalData<--method | Class CallTreeSet

## -- Q --

qualify | Probe Set Quality Control Functions
qualify.rlm | Probe Set Quality Control Functions
qualOption | Class QualTreeSet
qualOption-method | Class QualTreeSet
qualOption<- | Class QualTreeSet
qualOption<--method | Class QualTreeSet
QualTreeSet | Class QualTreeSet
QualTreeSet-class | Class QualTreeSet
qualType | Class QualTreeSet
qualType-method | Class QualTreeSet
qualType<- | Class QualTreeSet
qualType<--method | Class QualTreeSet
quantileFilter | Quantile Filter
quantileFilter-method | Class PreFilter
quantileFilter-methods | Quantile Filter
quantileFilter<- | Quantile Filter
quantileFilter<--method | Class PreFilter

## -- R --

ratioFilter | Ratio Filter
ratioFilter-method | Class PreFilter
ratioFilter-methods | Ratio Filter
ratioFilter<- | Ratio Filter
ratioFilter<--method | Class PreFilter
rawCELName | Method for getting names of the raw CEL-files
rawCELName-method | Class DataTreeSet
rawCELName-methods | Method for getting names of the raw CEL-files
removeBgrd | Attach/Remove Background Intensities
removeBgrd-method | Class DataTreeSet
removeBgrd-methods | Attach/Remove Background Intensities
removeCall | Attach/Remove Detecion Call Measures
removeCall-method | Class CallTreeSet
removeCall-methods | Attach/Remove Detecion Call Measures
removeData | Attach/Remove Data
removeData-method | Class ProcesSet
removeData-methods | Attach/Remove Data
removeDataXY | Attach/Remove (X,Y)-Coordinates
removeDataXY-method | Class DataTreeSet
removeDataXY-methods | Attach/Remove (X,Y)-Coordinates
removeExpr | Attach/Remove Expression Measures
removeExpr-method | Class ExprTreeSet
removeExpr-methods | Attach/Remove Expression Measures
removeInten | Attach/Remove Intensities
removeInten-method | Class DataTreeSet
removeInten-methods | Attach/Remove Intensities
removeMask | Attach/Remove Scheme Mask
removeMask-method | Class DataTreeSet
removeMask-method | Class SchemeTreeSet
removeMask-methods | Attach/Remove Scheme Mask
removeProbe | Attach/Remove Probe Sequence and/or GC Content
removeProbe-method | Class SchemeTreeSet
removeProbeContentGC | Attach/Remove Probe Sequence and/or GC Content
removeProbeContentGC-method | Class DataTreeSet
removeProbeContentGC-method | Class SchemeTreeSet
removeProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content
removeProbeSequence | Attach/Remove Probe Sequence and/or GC Content
removeProbeSequence-method | Class SchemeTreeSet
removeProbeSequence-methods | Attach/Remove Probe Sequence and/or GC Content
removePVal | Attach/Remove Detecion Call Measures
removePVal-method | Class CallTreeSet
removePVal-methods | Attach/Remove Detecion Call Measures
removeUnitNames | Attach/Remove Unit Names
removeUnitNames-method | Class DataTreeSet
removeUnitNames-method | Class SchemeTreeSet
removeUnitNames-methods | Attach/Remove Unit Names
residuals | Class QualTreeSet
residuals-method | Class QualTreeSet
RLE | Relative Log Expression (RLE)
RLE-method | Class QualTreeSet
RLE-methods | Relative Log Expression (RLE)
rleplot | Box Plots of Relative Log Expression (RLE)
rleplot-method | Class ExprTreeSet
rleplot-method | Class QualTreeSet
rleplot-methods | Box Plots of Relative Log Expression (RLE)
rma | Robust Multi-Array Average Expression Measure
rmaPLM | Functions for fitting RMA as probe-level model
ROOT | ROOT An Object-Oriented Data Analysis Framework
root.browser | Open the ROOT object browser
root.browser-method | Class TreeSet
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
rootFile | Class TreeSet
rootFile-method | Class TreeSet
rootFile<- | Class TreeSet
rootFile<--method | Class TreeSet

## -- S --

sampleInfo | Class ProjectInfo
sampleInfo-method | Class ProjectInfo
sampleInfo<- | Class ProjectInfo
sampleInfo<--method | Class ProjectInfo
schemeFile | Class ProcesSet
schemeFile-method | Class ProcesSet
schemeFile<- | Class ProcesSet
schemeFile<--method | Class ProcesSet
schemeSet | Class ProcesSet
schemeSet-method | Class ProcesSet
schemeSet<- | Class ProcesSet
schemeSet<--method | Class ProcesSet
SchemeTreeSet | Class SchemeTreeSet
SchemeTreeSet-class | Class SchemeTreeSet
se.exprs | Class ExprTreeSet
se.exprs-method | Class ExprTreeSet
setName | Class TreeSet
setName-method | Class TreeSet
setName<- | Class TreeSet
setName<--method | Class TreeSet
setType | Class TreeSet
setType-method | Class TreeSet
setType<- | Class TreeSet
setType<--method | Class TreeSet
show-method | Class ProjectInfo
sourceInfo | Class ProjectInfo
sourceInfo-method | Class ProjectInfo
sourceInfo<- | Class ProjectInfo
sourceInfo<--method | Class ProjectInfo
summarize | Probe Set Summarizing Functions
summarize.mas4 | Probe Set Summarizing Functions
summarize.mas5 | Probe Set Summarizing Functions
summarize.rma | Probe Set Summarizing Functions
summaryAffyRNAdeg | Functions to assess RNA Degradation.
symbol2unitID | Conversion between Gene Symbols and UnitIDs
symbol2unitID-method | Class DataTreeSet
symbol2unitID-method | Class SchemeTreeSet
symbol2unitID-methods | Conversion between Gene Symbols and UnitIDs

## -- T --

tissueInfo | Class ProjectInfo
tissueInfo-method | Class ProjectInfo
tissueInfo<- | Class ProjectInfo
tissueInfo<--method | Class ProjectInfo
transcriptID2unitID | Conversion between Probeset IDs and UnitIDs
transcriptID2unitID-method | Class DataTreeSet
transcriptID2unitID-method | Class SchemeTreeSet
transcriptID2unitID-methods | Conversion between Probeset IDs and UnitIDs
treatmentInfo | Class ProjectInfo
treatmentInfo-method | Class ProjectInfo
treatmentInfo<- | Class ProjectInfo
treatmentInfo<--method | Class ProjectInfo
treeData | Class ProcesSet
treeData-method | Class ProcesSet
treeInfo | Get UserInfo from ROOT Trees
treeInfo-method | Class TreeSet
treeInfo-methods | Get UserInfo from ROOT Trees
treeNames | Class TreeSet
treeNames-method | Class TreeSet
TreeSet | Class TreeSet
TreeSet-class | Class TreeSet
trma | transposed Robust Multi-Array Average Expression Measure
type2Exten | Convert Method Type to Tree Extension

## -- U --

UniFilter | Constructor for Class UniFilter
unifilter | Function for Applying an UniFilter to an ExprTreeSet
UniFilter-class | Class UniFilter
uniTest | A Two-Group Unitest
uniTest-method | Class UniFilter
uniTest-methods | A Two-Group Unitest
uniTest<- | A Two-Group Unitest
uniTest<--method | Class UniFilter
unitestFilter | Unitest Filter
unitestFilter-method | Class UniFilter
unitestFilter-methods | Unitest Filter
unitestFilter<- | Unitest Filter
unitestFilter<--method | Class UniFilter
unitID2probesetID | Conversion between Probeset IDs and UnitIDs
unitID2probesetID-method | Class DataTreeSet
unitID2probesetID-method | Class SchemeTreeSet
unitID2probesetID-methods | Conversion between Probeset IDs and UnitIDs
unitID2symbol | Conversion between Gene Symbols and UnitIDs
unitID2symbol-method | Class DataTreeSet
unitID2symbol-method | Class SchemeTreeSet
unitID2symbol-methods | Conversion between Gene Symbols and UnitIDs
unitID2transcriptID | Conversion between Probeset IDs and UnitIDs
unitID2transcriptID-method | Class DataTreeSet
unitID2transcriptID-method | Class SchemeTreeSet
unitID2transcriptID-methods | Conversion between Probeset IDs and UnitIDs
unitNames | Class SchemeTreeSet
unitNames-method | Class SchemeTreeSet
unitNames<- | Class SchemeTreeSet
unitNames<--method | Class SchemeTreeSet

## -- V --

validBgrd | Class DataTreeSet
validBgrd-method | Class DataTreeSet
validCall | Get Valid Detection Call Values
validCall-method | Class CallTreeSet
validData | Extract Subset of Data
validData-method | Class AnalysisTreeSet
validData-method | Class DataTreeSet
validData-method | Class FilterTreeSet
validData-method | Class ProcesSet
validExpr | Get Valid Expression Levels
validExpr-method | Class ExprTreeSet
validFilter | Class AnalysisTreeSet
validFilter-method | Class AnalysisTreeSet
validPVal | Get Valid Detection Call Values
validPVal-method | Class CallTreeSet
validSE | Get Valid Standard Errors
validSE-method | Class ExprTreeSet
validTreetype | Validate Tree Type
varFilter | Variance Filter
varFilter-method | Class PreFilter
varFilter-methods | Variance Filter
varFilter<- | Variance Filter
varFilter<--method | Class PreFilter
volcanoplot | Volcano Plot
volcanoplot-method | Class AnalysisTreeSet
volcanoplot-methods | Volcano Plot

## -- W --

weights | Class QualTreeSet
weights-method | Class QualTreeSet

## -- X --

xps | xps Package Overview
xpsBgCorrect | Background Correction
xpsBgCorrect-method | Class DataTreeSet
xpsBgCorrect-methods | Background Correction
xpsDABGCall | Detection Above Background Call
xpsDABGCall-method | Class DataTreeSet
xpsDABGCall-methods | Detection Above Background Call
xpsFIRMA | Finding Isoforms using Robust Multichip Analysis
xpsFIRMA-method | Class DataTreeSet
xpsFIRMA-methods | Finding Isoforms using Robust Multichip Analysis
xpsINICall | Informative/Non-Informative Call
xpsINICall-method | Class DataTreeSet
xpsINICall-methods | Informative/Non-Informative Call
xpsMAS4 | MAS 4.0 Expression Measure
xpsMAS4-method | Class DataTreeSet
xpsMAS4-methods | MAS 4.0 Expression Measure
xpsMAS5 | MAS 5.0 Expression Measure
xpsMAS5-method | Class DataTreeSet
xpsMAS5-methods | MAS 5.0 Expression Measure
xpsMAS5Call | MAS 5.0 Absolute Detection Call
xpsMAS5Call-method | Class DataTreeSet
xpsMAS5Call-methods | MAS 5.0 Absolute Detection Call
xpsNormalize | Normalization on Affymetrix Probe Level Data or on Expression Levels
xpsNormalize-method | Class DataTreeSet
xpsNormalize-method | Class ExprTreeSet
xpsNormalize-methods | Normalization on Affymetrix Probe Level Data or on Expression Levels
xpsOptions | xps Options
xpsPreFilter | Function for Applying a PreFilter to an ExprTreeSet
xpsPreFilter-method | Class ExprTreeSet
xpsPreFilter-methods | Function for Applying a PreFilter to an ExprTreeSet
xpsPreprocess | Compute expression levels from raw data
xpsPreprocess-method | Class DataTreeSet
xpsPreprocess-methods | Compute expression levels from raw data
xpsQAReport | Create Quality Assessment Report.
xpsQualify | Probe Set Quality Control Functions
xpsQualify-method | Class DataTreeSet
xpsQualify-methods | Probe Set Quality Control Functions
xpsQualityControl | Functions for fitting probe-level models
xpsQualityControl-method | Class DataTreeSet
xpsQualityControl-methods | Functions for fitting probe-level models
xpsRMA | Robust Multi-Array Average Expression Measure
xpsRMA-method | Class DataTreeSet
xpsRMA-methods | Robust Multi-Array Average Expression Measure
xpsRNAdeg | Functions to assess RNA Degradation.
xpsRNAdeg-method | Class QualTreeSet
xpsRNAdeg-methods | Functions to assess RNA Degradation.
xpsSummarize | Probe Set Summarizing Functions
xpsSummarize-method | Class DataTreeSet
xpsSummarize-methods | Probe Set Summarizing Functions
xpsUniFilter | Function for Applying an UniFilter to an ExprTreeSet
xpsUniFilter-method | Class ExprTreeSet
xpsUniFilter-methods | Function for Applying an UniFilter to an ExprTreeSet