limma-package	01Introduction
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.GeneSetTests	10GeneSetTests
11.RNAseq	11RNAseq
alias2Symbol	alias2Symbol
alias2SymbolTable	alias2Symbol
alias2SymbolUsingNCBI	alias2Symbol
anova.MAList	anova-method
array2channel	targetsA2C
arrayWeights	arrayWeights
arrayWeightsQuick	arrayWeightsQuick
arrayWeightsSimple	arrayWeights
as.data.frame.EList	asdataframe
as.data.frame.EListRaw	asdataframe
as.data.frame.MAList	asdataframe
as.data.frame.MArrayLM	asdataframe
as.MAList	asmalist
as.matrix.EList	asmatrix
as.matrix.EListRaw	asmatrix
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
avearrays	avearrays
avearrays.default	avearrays
avearrays.EList	avearrays
avearrays.MAList	avearrays
avedups	avedups
avedups.default	avedups
avedups.EList	avedups
avedups.MAList	avedups
avereps	avereps
avereps.default	avereps
avereps.EList	avereps
avereps.EListRaw	avereps
avereps.MAList	avereps
avereps.RGList	avereps
backgroundCorrect	backgroundcorrect
backgroundCorrect.matrix	backgroundcorrect
barcodeplot	barcodeplot
beadCountWeights	beadCountWeights
blockDiag	blockDiag
bwss	bwss
bwss.matrix	bwss.matrix
camera	camera
camera.default	camera
cbind	cbind
cbind.EList	cbind
cbind.EListRaw	cbind
cbind.MAList	cbind
cbind.RGList	cbind
changeLog	changelog
classifyTestsF	classifytests
classifyTestsP	classifytests
classifyTestsT	classifytests
coerce,RGList,exprSet2-method	rglist
contrastAsCoef	contrastAsCoef
contrasts.fit	contrasts.fit
controlStatus	controlStatus
convest	propTrueNull
coolmap	coolmap
cumOverlap	cumOverlap
decideTests	decideTests
decideTests.default	decideTests
decideTests.MArrayLM	decideTests
designI2A	channel2M
designI2M	channel2M
detectionPValues	detectionPValue
detectionPValues.default	detectionPValue
detectionPValues.EListRaw	detectionPValue
diffSplice	diffSplice
dim.EList	dim
dim.EListRaw	dim
dim.MAList	dim
dim.MArrayLM	dim
dim.RGList	dim
dimnames.EList	dimnames
dimnames.EListRaw	dimnames
dimnames.MAList	dimnames
dimnames.MArrayLM	dimnames
dimnames.RGList	dimnames
dimnames<-.EList	dimnames
dimnames<-.EListRaw	dimnames
dimnames<-.MAList	dimnames
dimnames<-.RGList	dimnames
duplicateCorrelation	dupcor
eBayes	ebayes
ebayes	ebayes
EList-class	EList
EListRaw-class	EList
estimate.m0	propTrueNull
exprs.MA	exprsMA
fitFDist	fitfdist
fitFDistRobustly	fitfdist
fitGammaIntercept	fitGammaIntercept
fitmixture	fitmixture
fitted.MArrayLM	fitted.MArrayLM
fry	roast
fry.default	roast
FStat	classifytests
genas	genas
geneSetTest	geneSetTest
getDupSpacing	getlayout
getEAWP	getEAWP
getGeneKEGGLinks	goana
getKEGGPathwayNames	goana
getLayout	getlayout
getLayout2	getlayout
getSpacing	getSpacing
gls.series	gls.series
goana	goana
goana.default	goana
goana.MArrayLM	goana
gridc	gridspotrc
gridr	gridspotrc
heatDiagram	heatdiagram
heatdiagram	heatdiagram
helpMethods	helpMethods
ids2indices	ids2indices
imageplot	imageplot
imageplot3by2	imageplot3by2
interGeneCorrelation	camera
intraspotCorrelation	intraspotCorrelation
is.fullrank	isfullrank
isNumeric	isnumeric
kegga	goana
kegga.default	goana
kegga.MArrayLM	goana
kooperberg	kooperberg
LargeDataObject-class	LargeDataObject
length.EList	dim
length.EListRaw	dim
length.MAList	dim
length.MArrayLM	dim
length.RGList	dim
limma	01Introduction
limmaUsersGuide	limmaUsersGuide
lm.series	lm.series
lmFit	lmFit
lmscFit	lmscFit
loessFit	loessfit
logcosh	logcosh
MA.RG	normalizeWithinArrays
ma3x3.matrix	ma3x3
ma3x3.spottedarray	ma3x3
makeContrasts	makeContrasts
makeUnique	makeunique
MAList-class	malist
MArrayLM-class	marraylm
mdplot	mdplot
MDS-class	plotMDS
merge.EList	merge
merge.EListRaw	merge
merge.MAList	merge
merge.RGList	merge
mergeScans	mergeScansRG
mergeScansRG	mergeScansRG
modelMatrix	modelMatrix
modifyWeights	modifyWeights
mrlm	mrlm
mroast	roast
mroast.default	roast
nec	nec
neqc	nec
nonEstimable	isfullrank
normalizeBetweenArrays	normalizebetweenarrays
normalizeCyclicLoess	normalizeCyclicLoess
normalizeForPrintorder	normalizeprintorder
normalizeForPrintorder.rg	normalizeprintorder
normalizeMedianAbsValues	normalizeMedianAbsValues
normalizeMedianValues	normalizeMedianAbsValues
normalizeQuantiles	normalizequantiles
normalizeRobustSpline	normalizeRobustSpline
normalizeVSN	normalizeVSN
normalizeVSN.default	normalizeVSN
normalizeVSN.EListRaw	normalizeVSN
normalizeVSN.RGList	normalizeVSN
normalizeWithinArrays	normalizeWithinArrays
normexp.fit	normexpfit
normexp.fit.control	normexpfitcontrol
normexp.fit.detection.p	normexpfitdetectionp
normexp.signal	normexpsignal
plotDensities	plotDensities
plotDensities.default	plotDensities
plotDensities.EList	plotDensities
plotDensities.EListRaw	plotDensities
plotDensities.MAList	plotDensities
plotDensities.RGList	plotDensities
plotExons	plotExons
plotFB	plotFB
plotFB.default	plotFB
plotFB.EListRaw	plotFB
plotFB.RGList	plotFB
plotlines	plotlines
plotMA	plotma
plotMA.default	plotma
plotMA.EList	plotma
plotMA.EListRaw	plotma
plotMA.MAList	plotma
plotMA.MArrayLM	plotma
plotMA.RGList	plotma
plotMA3by2	plotma3by2
plotMD	plotMD
plotMD.default	plotMD
plotMD.EList	plotMD
plotMD.EListRaw	plotMD
plotMD.MAList	plotMD
plotMD.MArrayLM	plotMD
plotMD.RGList	plotMD
plotMDS	plotMDS
plotMDS.default	plotMDS
plotMDS.MDS	plotMDS
plotPrintorder	normalizeprintorder
plotPrintTipLoess	plotprinttiploess
plotRLDF	plotRLDF
plotSA	plotSA
plotSplice	plotSplice
plotWithHighlights	plotWithHighlights
poolVar	poolvar
predFCm	predFCm
printHead	printHead
PrintLayout-class	PrintLayout
printorder	printorder
printtipWeights	printtipWeights
printtipWeightsSimple	printtipWeights
propexpr	propexpr
propTrueNull	propTrueNull
protectMetachar	protectMetachar
qqf	qqt
qqt	qqt
QualityWeights	qualwt
rankSumTestWithCorrelation	rankSumTestwithCorrelation
rbind.EList	cbind
rbind.EListRaw	cbind
rbind.MAList	cbind
rbind.RGList	cbind
read.columns	read.columns
read.idat	read.idat
read.ilmn	read.ilmn
read.ilmn.targets	read.ilmn.targets
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
Roast-class	roast
roast.default	roast
romer	romer
romer.default	romer
selectModel	selectmodel
show,LargeDataObject-method	LargeDataObject
show,MDS-method	plotMDS
show,Roast-method	roast
show,TestResults-method	TestResults
spotc	gridspotrc
spotr	gridspotrc
squeezeVar	squeezeVar
strsplit2	strsplit2
subsetListOfArrays	subsetting
subsetting	subsetting
summary.EList	summary
summary.EListRaw	summary
summary.MAList	summary
summary.MArrayLM	summary
summary.RGList	summary
summary.TestResults	TestResults
targetsA2C	targetsA2C
TestResults-class	TestResults
tmixture.matrix	tmixture
tmixture.vector	tmixture
topGO	topGO
topKEGG	topGO
topRomer	topRomer
topSplice	topSplice
topTable	toptable
toptable	toptable
topTableF	toptable
topTreat	toptable
treat	ebayes
tricubeMovingAverage	tricubeMovingAverage
trigammaInverse	trigammainverse
trimWhiteSpace	trimWhiteSpace
tZscore	zscore
uniquegenelist	uniquegenelist
uniqueTargets	modelMatrix
unwrapdups	unwrapdups
vennCounts	venn
vennDiagram	venn
volcanoplot	volcanoplot
voom	voom
vooma	vooma
voomaByGroup	vooma
voomWithQualityWeights	voomWithQualityWeights
weighted.median	weightedmedian
weightedLowess	weightedLowess
wilcoxGST	geneSetTest
write.fit	writefit
wtarea	qualwt
wtflags	qualwt
wtIgnore.Filter	qualwt
zscore	zscore
zscoreGamma	zscore
zscoreHyper	zscore
zscoreT	zscore
[.EList	subsetting
[.EListRaw	subsetting
[.MAList	subsetting
[.MArrayLM	subsetting
[.RGList	subsetting
