beadarray-package	beadarray-package
addFeatureData	addFeatureData
annotation	annotationInterface
annotation,beadLevelData-method	annotationInterface
annotation,ExpressionSetIllumina-method	annotationInterface
annotation<-,beadLevelData,character-method	annotationInterface
annotation<-,ExpressionSetIllumina,character-method	annotationInterface
arrayNames	deprecatedFunctions
arrayNames,BeadLevelList-method	class-BeadLevelList
ArrayWeights	class-limmaResults
ArrayWeights,limmaResults-method	class-limmaResults
ArrayWeights<-	class-limmaResults
ArrayWeights<-,limmaResults,numeric-method	class-limmaResults
backgroundCorrectSingleSection	backgroundCorrectSingleSection
BASH	BASH
BASHCompact	BASHCompact
BASHDiffuse	BASHDiffuse
BASHExtended	BASHExtended
beadarrayUsersGuide	beadarrayUsersGuide
beadLevelData-class	class-beadLevelData
BeadLevelList-class	class-BeadLevelList
beadRegistrationData-class	class-beadRegistrationData
beadStatusVector	identifyControlBeads
boxplot,beadLevelData-method	class-beadLevelData
boxplot,beadRegistrationData-method	class-beadRegistrationData
boxplot,ExpressionSetIllumina-method	boxplot
calculateDetection	calculateDetection
calculateOutlierStats	calculateOutlierStats
checkPlatform	deprecatedFunctions
checkRegistration	checkRegistration
combine,beadLevelData,beadLevelData-method	combine
combine,ExpressionSetIllumina,ExpressionSetIllumina-method	combine
combinedControlPlot	expressionQCPipeline
ContrastMatrix	class-limmaResults
ContrastMatrix,limmaResults-method	class-limmaResults
ContrastMatrix<-	class-limmaResults
ContrastMatrix<-,limmaResults,matrix-method	class-limmaResults
controlProbeDetection	controlProbeDetection
convertBeadLevelList	convertBeadLevelList
createBeadSummaryData	deprecatedFunctions
createGEOMatrix	GEO
createGEOMeta	GEO
createTargetsFile	createTargetsFile
DesignMatrix	class-limmaResults
DesignMatrix,limmaResults-method	class-limmaResults
DesignMatrix<-	class-limmaResults
DesignMatrix<-,limmaResults,matrix-method	class-limmaResults
Detection	class-ExpressionSetIllumina
Detection,ExpressionSetIllumina-method	class-ExpressionSetIllumina
Detection<-	class-ExpressionSetIllumina
Detection<-,ExpressionSetIllumina,matrix-method	class-ExpressionSetIllumina
dim,beadLevelData-method	dim
dim,ExpressionSetIllumina-method	dim
dim,limmaResults-method	class-limmaResults
expressionQCPipeline	expressionQCPipeline
ExpressionSetIllumina-class	class-ExpressionSetIllumina
exprs,ExpressionSetIllumina-method	class-ExpressionSetIllumina
exprs<-,ExpressionSetIllumina,matrix-method	class-ExpressionSetIllumina
generateNeighbours	generateNeighbours
genericBeadIntensityPlot	plotBeadIntensities
getAnnotation	deprecatedFunctions
getArrayData	deprecatedFunctions
getArrayData,BeadLevelList-method	class-BeadLevelList
getBeadData	getBeadData
getControlProfile	annotationInterface
greenChannel	class-illuminaChannel
greenChannelTransform	transformationFunctions
HULK	HULK
identifyControlBeads	identifyControlBeads
illuminaBackground	imageProcessing
illuminaChannel-class	class-illuminaChannel
illuminaForeground	imageProcessing
illuminaOutlierMethod	illuminaOutlierMethod
illuminaSharpen	imageProcessing
imageplot	imageplot
insertBeadData	insertBeadData
insertSectionData	insertSectionData
limmaDE	limmaDE
limmaResults-class	class-limmaResults
LogFC	class-limmaResults
LogFC,limmaResults-method	class-limmaResults
LogFC<-	class-limmaResults
LogFC<-,limmaResults,matrix-method	class-limmaResults
logGreenChannelTransform	transformationFunctions
LogOdds	class-limmaResults
LogOdds,limmaResults-method	class-limmaResults
LogOdds<-	class-limmaResults
LogOdds<-,limmaResults,matrix-method	class-limmaResults
logRatioTransform	transformationFunctions
logRedChannelTransform	transformationFunctions
makeControlProfile	makeControlProfile
makeGEOSubmissionFiles	GEO
makeQCTable	makeQCTable
medianBackground	imageProcessing
medianNormalise	medianNormalise
metaTemplate	GEOtemplate
metrics	metrics
metrics,beadLevelData-method	metrics
nObservations	class-ExpressionSetIllumina
nObservations,ExpressionSetIllumina-method	class-ExpressionSetIllumina
nObservations<-	class-ExpressionSetIllumina
nObservations<-,ExpressionSetIllumina,matrix-method	class-ExpressionSetIllumina
noOutlierMethod	noOutlierMethod
normaliseIllumina	normaliseIllumina
numBeads	numBeads
numBeads,beadLevelData-method	class-beadLevelData
outlierplot	outlierplot
p95	metrics
p95,beadLevelData,character-method	metrics
platformSigs	platformSigs
plot,limmaResults-method	class-limmaResults
plotBeadIntensities	plotBeadIntensities
plotBeadLocations	plotBeadLocations
plotChipLayout	plotChipLayout
plotMA	plotMAXY
plotMA,ExpressionSetIllumina-method	maplots
plotMAXY	plotMAXY
plotTIFF	plotTIFF
plotXY	plotMAXY
poscontPlot	poscontPlot
processSwathData	processSwathData
PValue	class-limmaResults
PValue,limmaResults-method	class-limmaResults
PValue<-	class-limmaResults
PValue<-,limmaResults,matrix-method	class-limmaResults
qcData	class-ExpressionSetIllumina
qcData,ExpressionSetIllumina-method	class-ExpressionSetIllumina
quickSummary	quickSummary
readBeadSummaryData	readBeadSummaryData
readIdatFiles	readIdatFiles
readIllumina	readIllumina
readLocsFile	readLocsFile
readSampleSheet	sampleSheet
readTIFF	readTIFF
redChannelTransform	transformationFunctions
removeBeadData	insertBeadData
sampleSheet	sampleSheet
sampleSheet,beadLevelData-method	sampleSheet
sampleSheet,ExpressionSetIllumina-method	sampleSheet
sampleSheet<-	sampleSheet
sampleSheet<-,beadLevelData,data.frame-method	sampleSheet
sampleSheet<-,ExpressionSetIllumina,data.frame-method	sampleSheet
se.exprs,ExpressionSetIllumina-method	class-ExpressionSetIllumina
se.exprs<-,ExpressionSetIllumina,matrix-method	class-ExpressionSetIllumina
sectionNames	sectionNames
sectionNames,beadLevelData-method	class-beadLevelData
setAnnotation	deprecatedFunctions
setWeights	setWeights
show,beadLevelData-method	show
show,beadRegistrationData-method	show
show,ExpressionSetIllumina-method	show
show,limmaResults-method	show
showArrayMask	showArrayMask
snr	metrics
snr,beadLevelData,character-method	metrics
squeezedVarOutlierMethod	squeezedVarOutlierMethod
suggestAnnotation	annotationInterface
summarize	summarize
weightsOutlierMethod	weightsOutlierMethod
[,ExpressionSetIllumina,ANY-method	class-ExpressionSetIllumina
[,ExpressionSetIllumina-method	class-ExpressionSetIllumina
[,limmaResults-method	class-limmaResults
[[,beadLevelData,ANY,missing-method	class-beadLevelData
