oligo-package	oligo-package
annotation,oligoPLM-method	oligoPLM-class
availProbeInfo	getProbeInfo
backgroundCorrect	preprocessTools
backgroundCorrect,FeatureSet-method	preprocessTools
backgroundCorrect,ff_matrix-method	preprocessTools
backgroundCorrect,matrix-method	preprocessTools
backgroundCorrect-methods	preprocessTools
backgroundCorrectionMethods	preprocessTools
basecontent	basecontent
basicPLM	basicPLM
basicRMA	basicRMA
bg	IntensityMatrix-methods
bg,FeatureSet-method	IntensityMatrix-methods
bg,TilingFeatureSet-method	IntensityMatrix-methods
bg<-	IntensityMatrix-methods
bg<-,FeatureSet,ff_matrix-method	IntensityMatrix-methods
bg<-,FeatureSet,matrix-method	IntensityMatrix-methods
bg<-,TilingFeatureSet,array-method	IntensityMatrix-methods
bgindex	Index-methods
bgindex,DBPDInfo-method	Index-methods
bgindex,FeatureSet-method	Index-methods
bgSequence	Sequences-methods
bgSequence,DBPDInfo-method	Sequences-methods
bgSequence,ExonFeatureSet-method	Sequences-methods
bgSequence,FeatureSet-method	Sequences-methods
bgSequence,GeneFeatureSet-method	Sequences-methods
boxplot	boxplot
boxplot,ExpressionSet-method	boxplot
boxplot,FeatureSet-method	boxplot
boxplot,oligoPLM-method	oligoPLM-class
boxplot,PLMset-method	boxplot
boxplot-methods	boxplot
chromosome	chromosome
chromosome<-	chromosome
chromosome<-,AnnotatedDataFrame,character-method	chromosome
cleanPlatformName	read.celfiles
coef,oligoPLM-method	oligoPLM-class
coefs	oligoDefunct
coefs.probe	oligoPLM-class
coefs.probe,oligoPLM-method	oligoPLM-class
crlmm	crlmm
darkColors	colors
divColors	colors
fitPLM	oligoDefunct
fitProbeLevelModel	fitProbeLevelModel
geometry,oligoPLM-method	oligoPLM-class
getAffinitySplineCoefficients	getAffinitySplineCoefficients
getBaseProfile	getBaseProfile
getContainer	getContainer
getContainer,TilingFeatureSet-method	getContainer
getContainer-methods	getContainer
getCrlmmSummaries	getCrlmmSummaries
getNetAffx	getNetAffx
getNetAffx,ExpressionSet-method	getNetAffx
getNetAffx-methods	getNetAffx
getNgsColorsInfo	getNgsColorsInfo
getPD	getPlatformDesign
getPlatformDesign	getPlatformDesign
getPlatformDesign,FeatureSet-method	getPlatformDesign
getProbeInfo	getProbeInfo
getX	coordinates
getX,DBPDInfo-method	coordinates
getX,FeatureSet-method	coordinates
getX-methods	coordinates
getY	coordinates
getY,DBPDInfo-method	coordinates
getY,FeatureSet-method	coordinates
getY-methods	coordinates
hist	hist
hist,ExpressionSet-method	hist
hist,FeatureSet-method	hist
hist-methods	hist
image	image
image,FeatureSet-method	image
image,oligoPLM-method	oligoPLM-class
image,PLMset-method	image
image-methods	image
intensity	IntensityMatrix-methods
intensity,FeatureSet-method	IntensityMatrix-methods
intensity<-	IntensityMatrix-methods
intensity<-,FeatureSet-method	IntensityMatrix-methods
justCRLMM	crlmm
justSNPRMA	justSNPRMA
list.xysfiles	list.xysfiles
manufacturer,oligoPLM-method	oligoPLM-class
MAplot	MAplot-methods
MAplot,ExpressionSet-method	MAplot-methods
MAplot,FeatureSet-method	MAplot-methods
MAplot,matrix-method	MAplot-methods
MAplot,PLMset-method	MAplot-methods
MAplot,TilingFeatureSet-method	MAplot-methods
MAplot-methods	MAplot-methods
method	oligoPLM-class
method,oligoPLM-method	oligoPLM-class
mm	IntensityMatrix-methods
mm,FeatureSet-method	IntensityMatrix-methods
mm,TilingFeatureSet-method	IntensityMatrix-methods
mm<-	IntensityMatrix-methods
mm<-,FeatureSet,ANY,ANY,ff_matrix-method	IntensityMatrix-methods
mm<-,FeatureSet,ANY,ANY,matrix-method	IntensityMatrix-methods
mm<-,TilingFeatureSet,ANY,ANY,array-method	IntensityMatrix-methods
mmindex	Index-methods
mmindex,DBPDInfo-method	Index-methods
mmindex,FeatureSet-method	Index-methods
mmSequence	Sequences-methods
mmSequence,AffySNPPDInfo-method	Sequences-methods
mmSequence,DBPDInfo-method	Sequences-methods
mmSequence,FeatureSet-method	Sequences-methods
ncol,oligoPLM-method	oligoPLM-class
normalizationMethods	preprocessTools
normalize,FeatureSet-method	preprocessTools
normalize,ff_matrix-method	preprocessTools
normalize,matrix-method	preprocessTools
normalizeToTarget	preprocessTools
normalizeToTarget,ff_matrix-method	preprocessTools
normalizeToTarget,matrix-method	preprocessTools
normalizeToTarget-methods	preprocessTools
nprobes	oligoPLM-class
nprobes,oligoPLM-method	oligoPLM-class
nprobesets	oligoPLM-class
nprobesets,oligoPLM-method	oligoPLM-class
NUSE	oligoPLM-class
NUSE,oligoPLM-method	oligoPLM-class
oligo-defunct	oligoDefunct
oligoPLM	oligoPLM-class
oligoPLM-class	oligoPLM-class
opset2eset	oligoPLM-class
opset2eset,oligoPLM-method	oligoPLM-class
paCalls	paCalls
paCalls,ExonFeatureSet-method	paCalls
paCalls,ExpressionFeatureSet-method	paCalls
paCalls,GeneFeatureSet-method	paCalls
plotM	plotM-methods
plotM,SnpQSet,character-method	plotM-methods
plotM,SnpQSet,integer-method	plotM-methods
plotM,SnpQSet,numeric-method	plotM-methods
plotM,TilingQSet,missing-method	plotM-methods
plotM-methods	plotM-methods
pm	IntensityMatrix-methods
pm,FeatureSet-method	IntensityMatrix-methods
pm,GenericFeatureSet-method	IntensityMatrix-methods
pm,TilingFeatureSet-method	IntensityMatrix-methods
pm<-	IntensityMatrix-methods
pm<-,FeatureSet,ANY,ANY,ff_matrix-method	IntensityMatrix-methods
pm<-,FeatureSet,ANY,ANY,matrix-method	IntensityMatrix-methods
pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method	IntensityMatrix-methods
pm<-,GenericFeatureSet,ANY,ANY,matrix-method	IntensityMatrix-methods
pm<-,TilingFeatureSet,ANY,ANY,array-method	IntensityMatrix-methods
pmAllele	pmAllele
pmAllele,AffySNPPDInfo-method	pmAllele
pmAllele,SnpFeatureSet-method	pmAllele
pmChr	chromosome
pmChr,ExonFeatureSet-method	chromosome
pmChr,FeatureSet-method	chromosome
pmChr,GeneFeatureSet-method	chromosome
pmFragmentLength	pmFragmentLength
pmFragmentLength,AffySNPPDInfo-method	pmFragmentLength
pmFragmentLength,SnpFeatureSet-method	pmFragmentLength
pmindex	Index-methods
pmindex,DBPDInfo-method	Index-methods
pmindex,FeatureSet-method	Index-methods
pmindex,GenericFeatureSet-method	Index-methods
pmindex,GenericPDInfo-method	Index-methods
pmindex,stArrayDBPDInfo-method	Index-methods
pmOffset	pmPosition
pmOffset,AffySNPPDInfo-method	pmPosition
pmPosition	pmPosition
pmPosition,ExpressionPDInfo-method	pmPosition
pmPosition,FeatureSet-method	pmPosition
pmPosition,TilingFeatureSet-method	pmPosition
pmPosition,TilingPDInfo-method	pmPosition
pmSequence	Sequences-methods
pmSequence,AffyGenePDInfo-method	Sequences-methods
pmSequence,AffySNPPDInfo-method	Sequences-methods
pmSequence,DBPDInfo-method	Sequences-methods
pmSequence,ExonFeatureSet-method	Sequences-methods
pmSequence,FeatureSet-method	Sequences-methods
pmSequence,GeneFeatureSet-method	Sequences-methods
pmSequence,stArrayDBPDInfo-method	Sequences-methods
pmStrand	pmStrand
pmStrand,AffySNPPDInfo-method	pmStrand
pmStrand,TilingFeatureSet-method	pmStrand
probeNames	probeNames
probeNames,DBPDInfo-method	probeNames
probeNames,ExonFeatureSet-method	probeNames
probeNames,FeatureSet-method	probeNames
probeNames,GeneFeatureSet-method	probeNames
probeNames,stArrayDBPDInfo-method	probeNames
probesetNames	probeNames
probesetNames,FeatureSet-method	probeNames
read.celfiles	read.celfiles
read.celfiles2	read.celfiles
read.xysfiles	read.xysfiles
read.xysfiles2	read.xysfiles
readSummaries	readSummaries
resids	oligoDefunct
residuals,oligoPLM-method	oligoPLM-class
residualSE	oligoPLM-class
residualSE,oligoPLM-method	oligoPLM-class
RLE	oligoPLM-class
RLE,oligoPLM-method	oligoPLM-class
rma	rma-methods
rma,ExonFeatureSet-method	rma-methods
rma,ExpressionFeatureSet-method	rma-methods
rma,GeneFeatureSet-method	rma-methods
rma,GenericFeatureSet-method	rma-methods
rma,HTAFeatureSet-method	rma-methods
rma,SnpCnvFeatureSet-method	rma-methods
rma-methods	rma-methods
runDate	runDate
runDate,FeatureSet-method	runDate
runDate-methods	runDate
se	oligoPLM-class
se,oligoPLM-method	oligoPLM-class
se.probe	oligoPLM-class
se.probe,oligoPLM-method	oligoPLM-class
seqColors	colors
seqColors2	colors
sequenceDesignMatrix	sequenceDesignMatrix
show,oligoPLM-method	oligoPLM-class
snprma	snprma
summarizationMethods	preprocessTools
summarize	preprocessTools
summarize,ff_matrix-method	preprocessTools
summarize,matrix-method	preprocessTools
summarize-methods	preprocessTools
weights,oligoPLM-method	oligoPLM-class
