oligo-package	oligo-package
$,platformDesign-method	internals
AffySNPPDInfo-class	DBPDInfo-class
antisenseThetaA	snprmaSummaries
antisenseThetaA,SnpQSet-method	snprmaSummaries
antisenseThetaB	snprmaSummaries
antisenseThetaB,SnpQSet-method	snprmaSummaries
basecontent	basecontent
boxplot	boxplot
boxplot,ExpressionSet-method	boxplot
boxplot,FeatureSet-method	boxplot
cleanPlatformName	read.celfiles
crlmm	crlmm
db	internals
db,DBPDInfo-method	internals
db,SnpCallSet-method	internals
db,SnpCnvQSet-method	internals
db,SnpCopyNumberSet-method	internals
db,SnpFeatureSet-method	internals
db,SnpQSet-method	internals
DBPDInfo-class	DBPDInfo-class
ExonFeatureSet-class	FeatureSetExtensions-class
ExpressionFeatureSet-class	FeatureSetExtensions-class
exprs,FeatureSet-method	internals
featureIndex	featureIndex
featureIndex,FeatureSet-method	featureIndex
featureInfo	internals
featureInfo,platformDesign-method	internals
featureNames,FeatureSet-method	featureNames-methods
featureNames-methods	featureNames-methods
FeatureSet-class	FeatureSet-class
geneNames,AffySNPPDInfo-method	internals
geneNames,ExpressionPDInfo-method	internals
geneNames,FeatureSet-method	internals
geneNames,platformDesign-method	internals
geneNames,TilingPDInfo-method	internals
genomeBuild	genomeBuild
genomeBuild,PDInfo-method	genomeBuild
genomeBuild,TilingFeatureSet-method	genomeBuild
geometry	PDInfo-methods
geometry,PDInfo-method	PDInfo-methods
getA	SnpQSet-methods
getA,SnpCnvQSet-method	SnpQSet-methods
getA,SnpQSet-method	SnpQSet-methods
getChrXIndex	internals
getCrlmmSummaries	getCrlmmSummaries
getGenotypeRegionParams	internals
getM	SnpQSet-methods
getM,SnpCnvQSet-method	SnpQSet-methods
getM,SnpQSet-method	SnpQSet-methods
getPD	getPlatformDesign
getPlatformDesign	getPlatformDesign
getPlatformDesign,FeatureSet-method	getPlatformDesign
getSnpFragmentLength	internals
hist	hist
hist,ExpressionSet-method	hist
hist,FeatureSet-method	hist
image	image
image,FeatureSet-method	image
initialize,DBPDInfo-method	internals
initialize,FeatureSet-method	internals
initialize,SnpCallSet-method	internals
initialize,SnpCopyNumberSet-method	internals
initialize,SnpQSet-method	internals
justCRLMM	crlmm
justSNPRMA	justSNPRMA
kind	kind
kind,AffyExpressionPDInfo-method	kind
kind,AffyGenePDInfo-method	kind
kind,AffySNPCNVPDInfo-method	kind
kind,AffySNPPDInfo-method	kind
kind,ExpressionPDInfo-method	kind
kind,platformDesign-method	kind
kind,TilingPDInfo-method	kind
length,FeatureSet-method	internals
list.celfiles	list.celfiles
list.xysfiles	list.celfiles
listFeatureFields	PDInfo-methods
listFeatureFields,AffySNPPDInfo-method	PDInfo-methods
listFeatureFields,PDInfo-method	PDInfo-methods
listFeatureSetFields	PDInfo-methods
listFeatureSetFields,AffySNPPDInfo-method	PDInfo-methods
listFeatureSetFields,PDInfo-method	PDInfo-methods
manufacturer	manufacturer
manufacturer,FeatureSet-method	manufacturer
manufacturer,PDInfo-method	manufacturer
manufacturer<-	manufacturer
manufacturer<-,FeatureSet-method	manufacturer
MAplot	MAplot-methods
MAplot,FeatureSet-method	MAplot-methods
MAplot-methods	MAplot-methods
mm	IntensityMatrix-methods
mm,FeatureSet-method	IntensityMatrix-methods
mm<-	IntensityMatrix-methods
mm<-,FeatureSet,BufferedMatrix-method	IntensityMatrix-methods
mm<-,FeatureSet,matrix-method	IntensityMatrix-methods
mmindex	Index-methods
mmindex,AffySNPPDInfo-method	Index-methods
mmindex,ExpressionPDInfo-method	Index-methods
mmindex,FeatureSet-method	Index-methods
mmindex,platformDesign-method	Index-methods
mmindex,TilingPDInfo-method	Index-methods
mmSequence	Sequences-methods
mmSequence,AffySNPPDInfo-method	Sequences-methods
mmSequence,FeatureSet-method	Sequences-methods
mmSequence,platformDesign-method	Sequences-methods
names,platformDesign-method	internals
ncol	ncol
ncol,platformDesign-method	ncol
normalizeToSample	internals
nProbes	nProbes
nProbes,AffySNPPDInfo-method	nProbes
nProbes,ExpressionPDInfo-method	nProbes
nProbes,platformDesign-method	nProbes
nProbes,TilingPDInfo-method	nProbes
nrow	ncol
nrow,platformDesign-method	ncol
oligoSnpSet-class	SnpSetExtensions-class
PDInfo-class	PDInfo-class
platform	platform
platform,FeatureSet-method	platform
platform<-	platform
platform<-,FeatureSet-method	platform
platformDesign-class	platformDesign-class
platformDesignName	internals
platformDesignName,FeatureSet-method	internals
plotDensity	plotDensity
pm	IntensityMatrix-methods
pm,FeatureSet-method	IntensityMatrix-methods
pm,SnpCnvFeatureSet-method	IntensityMatrix-methods
pm<-	IntensityMatrix-methods
pm<-,FeatureSet,BufferedMatrix-method	IntensityMatrix-methods
pm<-,FeatureSet,matrix-method	IntensityMatrix-methods
pmAllele	pmAllele
pmAllele,AffySNPPDInfo-method	pmAllele
pmAllele,PDInfo-method	pmAllele
pmAllele,SnpFeatureSet-method	pmAllele
pmChr	chromosome
pmChr,TilingFeatureSet-method	chromosome
pmindex	Index-methods
pmindex,AffySNPCNVPDInfo-method	Index-methods
pmindex,AffySNPPDInfo-method	Index-methods
pmindex,ExpressionPDInfo-method	Index-methods
pmindex,FeatureSet-method	Index-methods
pmindex,platformDesign-method	Index-methods
pmindex,SnpCnvFeatureSet-method	Index-methods
pmindex,TilingPDInfo-method	Index-methods
pmOffset	pmPosition
pmOffset,AffySNPPDInfo-method	pmPosition
pmPosition	pmPosition
pmPosition,ExpressionPDInfo-method	pmPosition
pmPosition,TilingFeatureSet-method	pmPosition
pmPosition,TilingPDInfo-method	pmPosition
pmSequence	Sequences-methods
pmSequence,AffySNPCNVPDInfo-method	Sequences-methods
pmSequence,AffySNPPDInfo-method	Sequences-methods
pmSequence,ExpressionPDInfo-method	Sequences-methods
pmSequence,FeatureSet-method	Sequences-methods
pmSequence,platformDesign-method	Sequences-methods
pmSequence,TilingPDInfo-method	Sequences-methods
pmStrand	pmStrand
pmStrand,AffySNPPDInfo-method	pmStrand
position,SnpCallSet-method	pmPosition
position,TilingFeatureSet-method	pmPosition
probeNames	probeNames
probeNames,AffySNPPDInfo-method	probeNames
probeNames,ExpressionPDInfo-method	probeNames
probeNames,FeatureSet-method	probeNames
probeNames,platformDesign-method	probeNames
probeNames,TilingPDInfo-method	probeNames
read.celfiles	read.celfiles
read.xysfiles	read.xysfiles
readSummaries	readSummaries
rma	rma
rma,FeatureSet-method	rma
senseThetaA	snprmaSummaries
senseThetaA,SnpQSet-method	snprmaSummaries
senseThetaB	snprmaSummaries
senseThetaB,SnpQSet-method	snprmaSummaries
sequenceDesignMatrix	sequenceDesignMatrix
show,PDInfo-method	internals
show,platformDesign-method	internals
SnpCallSet-class	SnpSetExtensions-class
SnpCopyNumberSet-class	SnpSetExtensions-class
SnpFeatureSet-class	FeatureSetExtensions-class
SNPPDInfo-class	PDInfo-class
SnpQSet-class	SnpQSet-class
snprma	snprma
TilingFeatureSet-class	FeatureSetExtensions-class
[,FeatureSet-method	internals
