lumi-package	lumi.package
addAnnotationInfo	addAnnotationInfo
addControlData2lumi	addControlData2lumi
addControlData2methyLumiM	addControlData2methyLumiM
addNuID2lumi	addNuID2lumi
addNuId2lumi	addNuID2lumi
adjColorBias.quantile	adjColorBias.quantile
adjColorBias.ssn	adjColorBias.ssn
asBigMatrix	asBigMatrix-methods
asBigMatrix,ExpressionSet-method	asBigMatrix-methods
asBigMatrix-methods	asBigMatrix-methods
beadNum	LumiBatch-class
beadNum,ExpressionSet-method	LumiBatch-class
beadNum<-	LumiBatch-class
beadNum<-,ExpressionSet,ANY-method	LumiBatch-class
beadNum<-,ExpressionSet-method	LumiBatch-class
beta2m	beta2m
bgAdjust	bgAdjust
bgAdjustMethylation	bgAdjustMethylation
boxplot,ExpressionSet-method	boxplot-methods
boxplot,MethyLumiM-method	boxplot-MethyLumiM-methods
boxplot-methods	boxplot-methods
boxplot.ExpressionSet	boxplot-methods
boxplotColorBias	boxplotColorBias
class:LumiBatch	LumiBatch-class
colorBiasSummary	colorBiasSummary
combine,ExpressionSet,LumiBatch-method	LumiBatch-class
combine,LumiBatch,ExpressionSet-method	LumiBatch-class
combine,LumiBatch,LumiBatch-method	LumiBatch-class
controlData	LumiBatch-class
controlData,LumiBatch-method	LumiBatch-class
controlData<-	LumiBatch-class
controlData<-,LumiBatch,ANY-method	LumiBatch-class
controlData<-,LumiBatch-method	LumiBatch-class
density,ExpressionSet-method	density-methods
density-methods	density-methods
density.ExpressionSet	density-methods
detection	LumiBatch-class
detection,ExpressionSet-method	LumiBatch-class
detection<-	LumiBatch-class
detection<-,ExpressionSet,ANY-method	LumiBatch-class
detection<-,ExpressionSet-method	LumiBatch-class
detectionCall	detectionCall
detectOutlier	detectOutlier
estimateBeta	estimateBeta
estimateIntensity	estimateIntensity
estimateLumiCV	estimateLumiCV
estimateM	estimateM
estimateMethylationBG	estimateMethylationBG
example.lumi	example.lumi
example.lumiMethy	example.lumiMethy
example.methyTitration	example.methyTitration
gammaFitEM	gammaFitEM
getChipInfo	getChipInfo
getChrInfo	getChrInfo
getControlData	getControlData
getControlProbe	getControlProbe
getControlType	getControlType
getHistory	LumiBatch-class
getHistory,LumiBatch-method	LumiBatch-class
getNuIDMappingInfo	getNuIDMappingInfo
hist,ExpressionSet-method	hist-methods
hist-methods	hist-methods
hist.ExpressionSet	hist-methods
id2seq	id2seq
IlluminaID2nuID	IlluminaID2nuID
importMethyIDAT	importMethyIDAT
initialize,LumiBatch-method	LumiBatch-class
inverseVST	inverseVST
is.nuID	is.nuID
lumi	lumi.package
lumiB	lumiB
LumiBatch	LumiBatch-class
LumiBatch-class	LumiBatch-class
lumiExpresso	lumiExpresso
lumiMethyB	lumiMethyB
lumiMethyC	lumiMethyC
lumiMethyN	lumiMethyN
lumiMethyR	lumiMethyR
lumiMethyStatus	lumiMethyStatus
lumiN	lumiN
lumiQ	lumiQ
lumiR	lumiR
lumiR.batch	lumiR.batch
lumiT	lumiT
m2beta	m2beta
MAplot	MAplot-methods
MAplot,ExpressionSet-method	MAplot-methods
MAplot-methods	MAplot-methods
MAplot.ExpressionSet	MAplot-methods
methylationCall	methylationCall
monoSmu	monoSmu
monoSpline	monoSpline
normalizeMethylation.quantile	normalizeMethylation.quantile
normalizeMethylation.ssn	normalizeMethylation.ssn
nuID2EntrezID	nuID2EntrezID
nuID2IlluminaID	nuID2IlluminaID
nuID2probeID	nuID2probeID
nuID2RefSeqID	nuID2RefSeqID
nuID2targetID	nuID2targetID
pairs,ExpressionSet-method	pairs-methods
pairs-methods	pairs-methods
pairs.ExpressionSet	pairs-methods
plot,ExpressionSet,missing-method	plot-methods
plot,ExpressionSet-method	plot-methods
plot-methods	plot-methods
plot.ExpressionSet	plot-methods
plotCDF	plotCDF
plotCDF,ExpressionSet-method	plotCDF
plotCDF.ExpressionSet	plotCDF
plotColorBias1D	plotColorBias1D
plotColorBias2D	plotColorBias2D
plotControlData	plotControlData
plotDensity	plotDensity
plotDensity.ExpressionSet	plotDensity
plotGammaFit	plotGammaFit
plotHousekeepingGene	plotHousekeepingGene
plotSampleRelation	plotSampleRelation
plotStringencyGene	plotStringencyGene
plotVST	plotVST
probeID2nuID	probeID2nuID
produceGEOPlatformFile	produceGEOPlatformFile
produceGEOSampleInfoTemplate	produceGEOSampleInfoTemplate
produceGEOSubmissionFile	produceGEOSubmissionFile
produceMethylationGEOSubmissionFile	produceMethylationGEOSubmissionFile
rankinvariant	rankinvariant
rsn	rsn
sampleNames<-,LumiBatch,ANY-method	LumiBatch-class
se.exprs	LumiBatch-class
se.exprs,ExpressionSet-method	LumiBatch-class
se.exprs<-	LumiBatch-class
se.exprs<-,ExpressionSet,ANY-method	LumiBatch-class
se.exprs<-,ExpressionSet-method	LumiBatch-class
seq2id	seq2id
show,LumiBatch-method	LumiBatch-class
smoothQuantileNormalization	smoothQuantileNormalization
ssn	ssn
summary,LumiBatch-method	LumiBatch-class
targetID2nuID	targetID2nuID
vst	vst
[,LumiBatch,ANY,ANY,ANY-method	LumiBatch-class
[,LumiBatch-method	LumiBatch-class
