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

## Documentation for package ‘xps’ version 1.4.10

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- --

xps-package | xps Package Overview

## -- A --

addData | Import additional CEL files into a DataTreeSet
addData,DataTreeSet-method | Class DataTreeSet
addData-methods | Import additional CEL files into a DataTreeSet
AnalysisTreeSet | Class AnalysisTreeSet
AnalysisTreeSet-class | Class AnalysisTreeSet
arrayInfo | Class ProjectInfo
arrayInfo,ProjectInfo-method | Class ProjectInfo
arrayInfo<- | Class ProjectInfo
arrayInfo<-,ProjectInfo,character-method | Class ProjectInfo
attachBgrd | Attach/Remove Background Intensities
attachBgrd,DataTreeSet-method | Class DataTreeSet
attachBgrd-methods | Attach/Remove Background Intensities
attachCall | Attach/Remove Detecion Call Measures
attachCall,CallTreeSet-method | Class CallTreeSet
attachCall-methods | Attach/Remove Detecion Call Measures
attachExpr | Attach/Remove Expression Measures
attachExpr,ExprTreeSet-method | Class ExprTreeSet
attachExpr-methods | Attach/Remove Expression Measures
attachInten | Attach/Remove Intensities
attachInten,DataTreeSet-method | Class DataTreeSet
attachInten-methods | Attach/Remove Intensities
attachMask | Attach/Remove Scheme Mask
attachMask,DataTreeSet-method | Class DataTreeSet
attachMask,SchemeTreeSet-method | Class SchemeTreeSet
attachMask-methods | Attach/Remove Scheme Mask
attachPVal | Attach/Remove Detecion Call Measures
attachPVal,CallTreeSet-method | Class CallTreeSet
attachPVal-methods | Attach/Remove Detecion Call Measures
authorInfo | Class ProjectInfo
authorInfo,ProjectInfo-method | Class ProjectInfo
authorInfo<- | Class ProjectInfo
authorInfo<-,ProjectInfo,character-method | Class ProjectInfo

## -- B --

background | Class DataTreeSet
background,DataTreeSet-method | Class DataTreeSet
background<- | Class DataTreeSet
background<-,DataTreeSet,data.frame-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,DataTreeSet-method | Class DataTreeSet
biopsyInfo | Class ProjectInfo
biopsyInfo,ProjectInfo-method | Class ProjectInfo
biopsyInfo<- | Class ProjectInfo
biopsyInfo<-,ProjectInfo,character-method | Class ProjectInfo
boxplot | Box Plots
boxplot,ProcesSet-method | Class ProcesSet
boxplot-methods | Box Plots
boxplot.dev | Box Plots for Device

## -- C --

callFilter | Detection Call Filter
callFilter,PreFilter-method | Class PreFilter
callFilter,UniFilter-method | Class UniFilter
callFilter-methods | Detection Call Filter
callFilter<- | Detection Call Filter
callFilter<-,PreFilter,character-method | Class PreFilter
callFilter<-,UniFilter,character-method | Class UniFilter
callplot | Barplot of Percent Present and Absent Calls.
callplot,CallTreeSet-method | Class CallTreeSet
callplot-methods | Barplot of Percent Present and Absent Calls.
CallTreeSet | Class CallTreeSet
callTreeset | Class FilterTreeSet
callTreeset,FilterTreeSet-method | Class FilterTreeSet
CallTreeSet-class | Class CallTreeSet
cellineInfo | Class ProjectInfo
cellineInfo,ProjectInfo-method | Class ProjectInfo
cellineInfo<- | Class ProjectInfo
cellineInfo<-,ProjectInfo,character-method | Class ProjectInfo
chipMask | Class SchemeTreeSet
chipMask,SchemeTreeSet-method | Class SchemeTreeSet
chipMask<- | Class SchemeTreeSet
chipMask<-,SchemeTreeSet,data.frame-method | Class SchemeTreeSet
chipName | Class SchemeTreeSet
chipName,ProcesSet-method | Class ProcesSet
chipName,SchemeTreeSet-method | Class SchemeTreeSet
chipType | Class SchemeTreeSet
chipType,ProcesSet-method | Class ProcesSet
chipType,SchemeTreeSet-method | Class SchemeTreeSet
chipType<- | Class SchemeTreeSet
chipType<-,SchemeTreeSet,character-method | Class SchemeTreeSet
cvFilter | Coefficient of Variation Filter
cvFilter,PreFilter-method | Class PreFilter
cvFilter-methods | Coefficient of Variation Filter
cvFilter<- | Coefficient of Variation Filter
cvFilter<-,PreFilter,numeric-method | Class PreFilter

## -- D --

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

## -- E --

existsROOTFile | Test for Existing ROOT File
exonLevel | Conversion of Parameter exonlevel to Integer
export | Export data as text files
export,ProcesSet-method | Class ProcesSet
export,SchemeTreeSet-method | Class SchemeTreeSet
export,TreeSet-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,ExprTreeSet-method | Class ExprTreeSet
exprs-methods | Get/Set Expression Values
exprs<- | Get/Set Expression Values
exprs<-,ExprTreeSet,data.frame-method | Class ExprTreeSet
ExprTreeSet | Class ExprTreeSet
exprTreeset | Class FilterTreeSet
exprTreeset,FilterTreeSet-method | Class FilterTreeSet
ExprTreeSet-class | Class ExprTreeSet
exprType | Class ExprTreeSet
exprType,ExprTreeSet-method | Class ExprTreeSet
exprType<- | Class ExprTreeSet
exprType<-,ExprTreeSet,character-method | Class ExprTreeSet

## -- F --

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

## -- G --

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

## -- H --

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

## -- I --

image | Display an Image
image,DataTreeSet-method | Class DataTreeSet
image-methods | Display an Image
image.dev | Image for Device
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
ini.call | Informative/Non-Informative Call
initialize | Initialize Classes
initialize,AnalysisTreeSet-method | Initialize Classes
initialize,CallTreeSet-method | Initialize Classes
initialize,DataTreeSet-method | Initialize Classes
initialize,ExprTreeSet-method | Initialize Classes
initialize,Filter-method | Initialize Classes
initialize,FilterTreeSet-method | Initialize Classes
initialize,PreFilter-method | Initialize Classes
initialize,ProcesSet-method | Initialize Classes
initialize,ProjectInfo-method | Initialize Classes
initialize,SchemeTreeSet-method | Initialize Classes
initialize,TreeSet-method | Initialize Classes
initialize,UniFilter-method | Initialize Classes
initialize-methods | Initialize Classes
intensity | Get/Set Data Values
intensity,DataTreeSet-method | Class DataTreeSet
intensity-methods | Get/Set Data Values
intensity<- | Get/Set Data Values
intensity<-,DataTreeSet,data.frame-method | Class DataTreeSet
isROOTFile | Test for ROOT File

## -- L --

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

## -- M --

madFilter | Median Absolute Deviation Filter
madFilter,PreFilter-method | Class PreFilter
madFilter-methods | Median Absolute Deviation Filter
madFilter<- | Median Absolute Deviation Filter
madFilter<-,PreFilter,numeric-method | Class PreFilter
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,ProcesSet-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,DataTreeSet-method | Class DataTreeSet
mm-methods | Methods for accessing perfect matches and mismatches
mvaplot | M vs A Plot
mvaplot,ExprTreeSet-method | Class ExprTreeSet
mvaplot-methods | M vs A Plot
mvaplot.dev | MvA Scatter Plot for Device

## -- N --

ncols | Class SchemeTreeSet
ncols,DataTreeSet-method | Class DataTreeSet
ncols,SchemeTreeSet-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,ExprTreeSet-method | Class ExprTreeSet
normType<- | Class ExprTreeSet
normType<-,ExprTreeSet,character-method | Class ExprTreeSet
nrows | Class SchemeTreeSet
nrows,DataTreeSet-method | Class DataTreeSet
nrows,SchemeTreeSet-method | Class SchemeTreeSet
numberFilters | Base Class Filter
numberFilters,Filter-method | Base Class Filter

## -- P --

pm | Methods for accessing perfect matches and mismatches
pm,DataTreeSet-method | Class DataTreeSet
pm-methods | Methods for accessing perfect matches and mismatches
pmplot | Barplot of PM and MM Intensities.
pmplot,DataTreeSet-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,CallTreeSet-method | Class CallTreeSet
presCall-methods | Get/Set Present Call Values
presCall<- | Get/Set Present Call Values
presCall<-,CallTreeSet,data.frame-method | Class CallTreeSet
primcellInfo | Class ProjectInfo
primcellInfo,ProjectInfo-method | Class ProjectInfo
primcellInfo<- | Class ProjectInfo
primcellInfo<-,ProjectInfo,character-method | Class ProjectInfo
probeInfo | Class SchemeTreeSet
probeInfo,SchemeTreeSet-method | Class SchemeTreeSet
ProcesSet | Class ProcesSet
ProcesSet-class | Class ProcesSet
ProjectInfo | Constructor for Class ProjectInfo
projectInfo | Class ProjectInfo
projectInfo,DataTreeSet-method | Class DataTreeSet
projectInfo,ProjectInfo-method | Class ProjectInfo
ProjectInfo-class | Class ProjectInfo
projectInfo<- | Class ProjectInfo
projectInfo<-,DataTreeSet,ProjectInfo-method | Class DataTreeSet
projectInfo<-,ProjectInfo,character-method | Class ProjectInfo
pvalData | Get/Set Present Call Values
pvalData,CallTreeSet-method | Class CallTreeSet
pvalData-methods | Get/Set Present Call Values
pvalData<- | Get/Set Present Call Values
pvalData<-,CallTreeSet,data.frame-method | Class CallTreeSet

## -- Q --

quantileFilter | Quantile Filter
quantileFilter,PreFilter-method | Class PreFilter
quantileFilter-methods | Quantile Filter
quantileFilter<- | Quantile Filter
quantileFilter<-,PreFilter,numeric-method | Class PreFilter

## -- R --

ratioFilter | Ratio Filter
ratioFilter,PreFilter-method | Class PreFilter
ratioFilter-methods | Ratio Filter
ratioFilter<- | Ratio Filter
ratioFilter<-,PreFilter,numeric-method | Class PreFilter
rawCELName | Method for getting names of the raw CEL-files
rawCELName,DataTreeSet-method | Class DataTreeSet
rawCELName-methods | Method for getting names of the raw CEL-files
removeBgrd | Attach/Remove Background Intensities
removeBgrd,DataTreeSet-method | Class DataTreeSet
removeBgrd-methods | Attach/Remove Background Intensities
removeCall | Attach/Remove Detecion Call Measures
removeCall,CallTreeSet-method | Class CallTreeSet
removeCall-methods | Attach/Remove Detecion Call Measures
removeExpr | Attach/Remove Expression Measures
removeExpr,ExprTreeSet-method | Class ExprTreeSet
removeExpr-methods | Attach/Remove Expression Measures
removeInten | Attach/Remove Intensities
removeInten,DataTreeSet-method | Class DataTreeSet
removeInten-methods | Attach/Remove Intensities
removeMask | Attach/Remove Scheme Mask
removeMask,DataTreeSet-method | Class DataTreeSet
removeMask,SchemeTreeSet-method | Class SchemeTreeSet
removeMask-methods | Attach/Remove Scheme Mask
removePVal | Attach/Remove Detecion Call Measures
removePVal,CallTreeSet-method | Class CallTreeSet
removePVal-methods | Attach/Remove Detecion Call Measures
rma | Robust Multi-Array Average Expression Measure
ROOT | ROOT An Object-Oriented Data Analysis Framework
root.browser | Open the ROOT object browser
root.browser,TreeSet-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,TreeSet-method | Class TreeSet
rootFile<- | Class TreeSet
rootFile<-,TreeSet,character-method | Class TreeSet

## -- S --

sampleInfo | Class ProjectInfo
sampleInfo,ProjectInfo-method | Class ProjectInfo
sampleInfo<- | Class ProjectInfo
sampleInfo<-,ProjectInfo,character-method | Class ProjectInfo
schemeFile | Class ProcesSet
schemeFile,ProcesSet-method | Class ProcesSet
schemeFile<- | Class ProcesSet
schemeFile<-,ProcesSet,character-method | Class ProcesSet
schemeSet | Class ProcesSet
schemeSet,ProcesSet-method | Class ProcesSet
schemeSet<- | Class ProcesSet
schemeSet<-,ProcesSet,SchemeTreeSet-method | Class ProcesSet
SchemeTreeSet | Class SchemeTreeSet
SchemeTreeSet-class | Class SchemeTreeSet
se.exprs | Class ExprTreeSet
se.exprs,ExprTreeSet-method | Class ExprTreeSet
setName | Class TreeSet
setName,TreeSet-method | Class TreeSet
setName<- | Class TreeSet
setName<-,TreeSet,character-method | Class TreeSet
setType | Class TreeSet
setType,TreeSet-method | Class TreeSet
setType<- | Class TreeSet
setType<-,TreeSet,character-method | Class TreeSet
show,ProjectInfo-method | Class ProjectInfo
sourceInfo | Class ProjectInfo
sourceInfo,ProjectInfo-method | Class ProjectInfo
sourceInfo<- | Class ProjectInfo
sourceInfo<-,ProjectInfo,character-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

## -- T --

tissueInfo | Class ProjectInfo
tissueInfo,ProjectInfo-method | Class ProjectInfo
tissueInfo<- | Class ProjectInfo
tissueInfo<-,ProjectInfo,character-method | Class ProjectInfo
treatmentInfo | Class ProjectInfo
treatmentInfo,ProjectInfo-method | Class ProjectInfo
treatmentInfo<- | Class ProjectInfo
treatmentInfo<-,ProjectInfo,character-method | Class ProjectInfo
treeNames | Class TreeSet
treeNames,TreeSet-method | Class TreeSet
TreeSet | Class TreeSet
TreeSet-class | Class TreeSet
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,UniFilter-method | Class UniFilter
uniTest-methods | A Two-Group Unitest
uniTest<- | A Two-Group Unitest
uniTest<-,UniFilter,character-method | Class UniFilter
unitestFilter | Unitest Filter
unitestFilter,UniFilter-method | Class UniFilter
unitestFilter-methods | Unitest Filter
unitestFilter<- | Unitest Filter
unitestFilter<-,UniFilter,character-method | Class UniFilter

## -- V --

validBgrd | Class DataTreeSet
validBgrd,DataTreeSet-method | Class DataTreeSet
validCall | Class CallTreeSet
validCall,CallTreeSet-method | Class CallTreeSet
validData | Extract Subset of Data
validData,AnalysisTreeSet-method | Class AnalysisTreeSet
validData,DataTreeSet-method | Class DataTreeSet
validData,FilterTreeSet-method | Class FilterTreeSet
validData,ProcesSet-method | Class ProcesSet
validFilter | Class AnalysisTreeSet
validFilter,AnalysisTreeSet-method | Class AnalysisTreeSet
validTreetype | Validate Tree Type
varFilter | Variance Filter
varFilter,PreFilter-method | Class PreFilter
varFilter-methods | Variance Filter
varFilter<- | Variance Filter
varFilter<-,PreFilter,numeric-method | Class PreFilter
volcanoplot | Volcano Plot
volcanoplot,AnalysisTreeSet-method | Class AnalysisTreeSet
volcanoplot-methods | Volcano Plot

## -- X --

xps | xps Package Overview
xpsBgCorrect | Background Correction
xpsBgCorrect,DataTreeSet-method | Class DataTreeSet
xpsBgCorrect-methods | Background Correction
xpsDABGCall | Detection Above Background Call
xpsDABGCall,DataTreeSet-method | Class DataTreeSet
xpsDABGCall-methods | Detection Above Background Call
xpsINICall | Informative/Non-Informative Call
xpsINICall,DataTreeSet-method | Class DataTreeSet
xpsINICall-methods | Informative/Non-Informative Call
xpsMAS4 | MAS 4.0 Expression Measure
xpsMAS4,DataTreeSet-method | Class DataTreeSet
xpsMAS4-methods | MAS 4.0 Expression Measure
xpsMAS5 | MAS 5.0 Expression Measure
xpsMAS5,DataTreeSet-method | Class DataTreeSet
xpsMAS5-methods | MAS 5.0 Expression Measure
xpsMAS5Call | MAS 5.0 Absolute Detection Call
xpsMAS5Call,DataTreeSet-method | Class DataTreeSet
xpsMAS5Call-methods | MAS 5.0 Absolute Detection Call
xpsNormalize | Normalization on Affymetrix Probe Level Data or on Expression Levels
xpsNormalize,DataTreeSet-method | Class DataTreeSet
xpsNormalize,ExprTreeSet-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,ExprTreeSet-method | Class ExprTreeSet
xpsPreFilter-methods | Function for Applying a PreFilter to an ExprTreeSet
xpsPreprocess | Compute expression levels from raw data
xpsPreprocess,DataTreeSet-method | Class DataTreeSet
xpsPreprocess-methods | Compute expression levels from raw data
xpsRMA | Robust Multi-Array Average Expression Measure
xpsRMA,DataTreeSet-method | Class DataTreeSet
xpsRMA-methods | Robust Multi-Array Average Expression Measure
xpsSummarize | Probe Set Summarizing Functions
xpsSummarize,DataTreeSet-method | Class DataTreeSet
xpsSummarize-methods | Probe Set Summarizing Functions
xpsUniFilter | Function for Applying an UniFilter to an ExprTreeSet
xpsUniFilter,ExprTreeSet-method | Class ExprTreeSet
xpsUniFilter-methods | Function for Applying an UniFilter to an ExprTreeSet