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,FeatureSet-method	boxplot
calls	SnpCallSet-methods
calls,SnpCallSet-method	SnpCallSet-methods
calls<-	SnpCallSet-methods
calls<-,SnpCallSet,matrix-method	SnpCallSet-methods
callsConfidence	SnpCallSet-methods
callsConfidence,SnpCallSet-method	SnpCallSet-methods
callsConfidence<-	SnpCallSet-methods
callsConfidence<-,SnpCallSet,matrix-method	SnpCallSet-methods
chromosome	chromosome
chromosome,TilingFeatureSet-method	chromosome
cleanPlatformName	read.celfiles
cnConfidence	SnpCopyNumberSet-methods
cnConfidence,SnpCopyNumberSet-method	SnpCopyNumberSet-methods
cnConfidence<-	SnpCopyNumberSet-methods
cnConfidence<-,SnpCopyNumberSet,matrix-method	SnpCopyNumberSet-methods
copyNumber	SnpCopyNumberSet-methods
copyNumber,SnpCopyNumberSet-method	SnpCopyNumberSet-methods
copyNumber<-	SnpCopyNumberSet-methods
copyNumber<-,SnpCopyNumberSet,matrix-method	SnpCopyNumberSet-methods
crlmm	crlmm
db	internals
db,DBPDInfo-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
FeatureSet-class	FeatureSet-class
geneNames,AffySNPPDInfo-method	internals
geneNames,FeatureSet-method	internals
geneNames,platformDesign-method	internals
genomeBuild	genomeBuild
genomeBuild,PDInfo-method	genomeBuild
genomeBuild,TilingFeatureSet-method	genomeBuild
geometry	PDInfo-methods
geometry,PDInfo-method	PDInfo-methods
getA	SnpQSet-methods
getA,SnpQSet-method	SnpQSet-methods
getChrXIndex	internals
getGenotypeRegionParams	internals
getM	SnpQSet-methods
getM,SnpQSet-method	SnpQSet-methods
getPD	getPlatformDesign
getPlatformDesign	getPlatformDesign
getPlatformDesign,FeatureSet-method	getPlatformDesign
getSnpFragmentLength	internals
hist	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
kind	kind
kind,AffySNPPDInfo-method	kind
kind,platformDesign-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
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,FeatureSet-method	Index-methods
mmindex,platformDesign-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,platformDesign-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<-	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,AffySNPPDInfo-method	Index-methods
pmindex,FeatureSet-method	Index-methods
pmindex,platformDesign-method	Index-methods
pmPosition	pmPosition
pmPosition,AffySNPPDInfo-method	pmPosition
pmPosition,TilingFeatureSet-method	pmPosition
pmSequence	Sequences-methods
pmSequence,AffySNPPDInfo-method	Sequences-methods
pmSequence,FeatureSet-method	Sequences-methods
pmSequence,platformDesign-method	Sequences-methods
pmStrand	pmStrand
pmStrand,AffySNPPDInfo-method	pmStrand
position	pmPosition
position,TilingFeatureSet-method	pmPosition
probeNames	probeNames
probeNames,AffySNPPDInfo-method	probeNames
probeNames,FeatureSet-method	probeNames
probeNames,platformDesign-method	probeNames
read.celfiles	read.celfiles
read.xysfiles	read.xysfiles
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
