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


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Documentation for package ‘xps’ version 1.28.0

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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