01.Introduction	01Introduction
02.Classes	02classes
03.ReadingData	03reading
04.Background	04Background
05.Normalization	05Normalization
06.LinearModels	06linearmodels
07.SingleChannel	07SingleChannel
08.Tests	08Tests
09.Diagnostics	09Diagnostics
10.Other	10Other
alias2Symbol	alias2Symbol
anova.MAList	anova-method
array2channel	targetsA2C
arrayWeights	arrayWeights
arrayWeightsQuick	arrayWeightsQuick
arrayWeightsSimple	arrayWeights
as.data.frame.MArrayLM	asdataframe
as.MAList	asmalist
as.matrix.ExpressionSet	asmatrix
as.matrix.LumiBatch	asmatrix
as.matrix.MAList	asmatrix
as.matrix.MArrayLM	asmatrix
as.matrix.marrayNorm	asmatrix
as.matrix.PLMset	asmatrix
as.matrix.RGList	asmatrix
as.matrix.vsn	asmatrix
asMatrixWeights	asMatrixWeights
auROC	auROC
avedups	avedups
avedups.default	avedups
avedups.MAList	avedups
avereps	avereps
avereps.default	avereps
avereps.MAList	avereps
backgroundCorrect	backgroundcorrect
barcodeplot	geneSetTest
blockDiag	blockDiag
bwss	bwss
bwss.matrix	bwss.matrix
cbind.MAList	cbind
cbind.RGList	cbind
changeLog	changelog
classifyTestsF	classifytests
classifyTestsP	classifytests
classifyTestsT	classifytests
coerce,RGList,exprSet2-method	rglist
contrasts.fit	contrasts.fit
controlStatus	controlStatus
convest	convest
decideTests	decideTests
designI2A	channel2M
designI2M	channel2M
dim.MAList	dim
dim.MArrayLM	dim
dim.RGList	dim
dimnames.MAList	dimnames
dimnames.MArrayLM	dimnames
dimnames.RGList	dimnames
dimnames<-.MAList	dimnames
dimnames<-.RGList	dimnames
duplicateCorrelation	dupcor
eBayes	ebayes
ebayes	ebayes
exprs.MA	exprsMA
fitFDist	fitfdist
fitted.MArrayLM	fitted.MArrayLM
FStat	classifytests
geneSetTest	geneSetTest
getDupSpacing	getlayout
getEAWP	getEAWP
getLayout	getlayout
getLayout2	getlayout
getSpacing	getSpacing
gls.series	gls.series
gridc	gridspotrc
gridr	gridspotrc
heatDiagram	heatdiagram
heatdiagram	heatdiagram
helpMethods	helpMethods
imageplot	imageplot
imageplot3by2	imageplot3by2
intraspotCorrelation	intraspotCorrelation
is.fullrank	isfullrank
isNumeric	isnumeric
kooperberg	kooperberg
LargeDataObject-class	LargeDataObject
length.MAList	dim
length.MArrayLM	dim
length.RGList	dim
limma	01Introduction
limmaUsersGuide	limmaUsersGuide
lm.series	lm.series
lmFit	lmFit
lmscFit	lmscFit
loessFit	loessfit
MA.RG	normalizeWithinArrays
ma3x3.matrix	ma3x3
ma3x3.spottedarray	ma3x3
makeContrasts	makeContrasts
makeUnique	makeunique
MAList-class	malist
MArrayLM-class	marraylm
mdplot	mdplot
merge.MAList	merge
merge.RGList	merge
mergeScans	mergeScansRG
mergeScansRG	mergeScansRG
modelMatrix	modelMatrix
modifyWeights	modifyWeights
mrlm	mrlm
nonEstimable	isfullrank
normalizeBetweenArrays	normalizebetweenarrays
normalizeForPrintorder	normalizeprintorder
normalizeForPrintorder.rg	normalizeprintorder
normalizeMedianAbsValues	normalizeMedianAbsValues
normalizeQuantiles	normalizequantiles
normalizeRobustSpline	normalizeRobustSpline
normalizeWithinArrays	normalizeWithinArrays
normexp.fit	normexpfit
normexp.signal	normexpsignal
plotDensities	plotDensities
plotFB	plotFB
plotlines	plotlines
plotMA	plotma
plotMA3by2	plotma3by2
plotPrintorder	normalizeprintorder
plotPrintTipLoess	plotprinttiploess
poolVar	poolvar
printHead	printHead
PrintLayout-class	PrintLayout
printorder	printorder
printtipWeights	printtipWeights
printtipWeightsSimple	printtipWeights
protectMetachar	protectMetachar
qqt	qqt
QualityWeights	qualwt
rbind.MAList	cbind
rbind.RGList	cbind
read.columns	read.columns
read.imagene	read.maimages
read.maimages	read.maimages
readGAL	readgal
readGenericHeader	readGPRHeader
readGPRHeader	readGPRHeader
readImaGeneHeader	readImaGeneHeader
readSMDHeader	readGPRHeader
readSpotTypes	readSpotTypes
readTargets	readTargets
removeBatchEffect	removeBatchEffect
removeExt	removeext
residuals.MArrayLM	residuals.MArrayLM
RG.MA	normalizeWithinArrays
RGList-class	rglist
roast	roast
selectModel	selectmodel
show,LargeDataObject-method	LargeDataObject
show,TestResults-method	TestResults
spotc	gridspotrc
spotr	gridspotrc
squeezeVar	squeezeVar
strsplit2	strsplit2
summary.MAList	summary
summary.MArrayLM	summary
summary.RGList	summary
summary.TestResults	TestResults
targetsA2C	targetsA2C
TestResults-class	TestResults
tmixture.matrix	tmixture
tmixture.vector	tmixture
topTable	toptable
toptable	toptable
topTableF	toptable
treat	ebayes
trigammaInverse	trigammainverse
trimWhiteSpace	trimWhiteSpace
tZscore	zscore
uniquegenelist	uniquegenelist
uniqueTargets	modelMatrix
unwrapdups	unwrapdups
vennCounts	venn
vennDiagram	venn
volcanoplot	volcanoplot
weighted.median	weightedmedian
write.fit	writefit
wtarea	qualwt
wtflags	qualwt
wtIgnore.Filter	qualwt
zscoreGamma	zscore
zscoreT	zscore
[.MAList	subsetting
[.MArrayLM	subsetting
[.RGList	subsetting
