API for limma
Linear Models for Microarray Data

Global functions
.arrayWeightsGeneByGene	Source code
.arrayWeightsPrWtsREML	Source code
.arrayWeightsREML	Source code
.bg.parameters.rma75	Source code
.classifyTestsP	Source code
.denominatorBayesianAdjustedFG	Source code
.ebayes	Source code
.expectedBayesianAdjustedFG	Source code
.fryEffects	Source code
.hockey	Source code
.ilmn.biological.variance	Source code
.lmEffects	Source code
.matvec	Source code
.meanHalf	Source code
.mergeScans1	Source code
.normalConvolution	Source code
.normexp.gm2loglik	Source code
.normexp.hm2loglik	Source code
.normexp.m2loglik	Source code
.numeratorBayesianAdjustedFG	Source code
.onAttach	Source code
.onLoad	Source code
.onUnload	Source code
.propTrueNullByLocalFDR	Source code
.propTrueNullByMeanP	Source code
.propTrueNullFromHistogram	Source code
.read.oneilmnfile	Source code
.roastEffects	Source code
.setdimnames	Source code
.squeezeVar	Source code
.topTableF	Source code
.topTableT	Source code
.vecmat	Source code
.zscoreTBailey	Source code
.zscoreTHill	Source code
.zscoreTQuantile	Source code
.zscoreTWallace	Source code
01.Introduction	Man page
02.Classes	Man page
03.ReadingData	Man page
04.Background	Man page
05.Normalization	Man page
06.LinearModels	Man page
07.SingleChannel	Man page
08.Tests	Man page
09.Diagnostics	Man page
10.GeneSetTests	Man page
11.RNAseq	Man page
EList-class	Man page
EListRaw-class	Man page
LargeDataObject-class	Man page
MA.RG	Man page Source code
MAList-class	Man page
MArrayLM-class	Man page
MDS-class	Man page
PrintLayout-class	Man page
QualityWeights	Man page
RG.MA	Man page Source code
RGList-class	Man page
Roast-class	Man page
TestResults-class	Man page
[.EList	Man page
[.EListRaw	Man page
[.MAList	Man page
[.MArrayLM	Man page
[.RGList	Man page
[.TestResults	Man page
alias2Symbol	Man page Source code
alias2SymbolTable	Man page Source code
alias2SymbolUsingNCBI	Man page Source code
anova.MAList	Man page Source code
array2channel	Man page
arrayWeights	Man page Source code
arrayWeightsQuick	Man page Source code
as.MAList	Man page Source code
as.data.frame.EList	Man page
as.data.frame.EListRaw	Man page Source code
as.data.frame.MAList	Man page Source code
as.data.frame.MArrayLM	Man page Source code
as.matrix.EList	Man page Source code
as.matrix.EListRaw	Man page
as.matrix.ExpressionSet	Man page
as.matrix.LumiBatch	Man page Source code
as.matrix.MAList	Man page Source code
as.matrix.MArrayLM	Man page Source code
as.matrix.PLMset	Man page Source code
as.matrix.RGList	Man page Source code
as.matrix.marrayNorm	Man page Source code
as.matrix.vsn	Man page Source code
asMatrixWeights	Man page Source code
auROC	Man page Source code
avearrays	Man page Source code
avearrays.EList	Man page Source code
avearrays.MAList	Man page Source code
avearrays.default	Man page Source code
avedups	Man page Source code
avedups.EList	Man page Source code
avedups.MAList	Man page Source code
avedups.default	Man page Source code
avereps	Man page Source code
avereps.EList	Man page Source code
avereps.EListRaw	Man page Source code
avereps.MAList	Man page Source code
avereps.RGList	Man page Source code
avereps.default	Man page Source code
backgroundCorrect	Man page Source code
backgroundCorrect.matrix	Man page Source code
barcodeplot	Man page
beadCountWeights	Man page Source code
blockDiag	Man page Source code
bwss	Man page Source code
bwss.matrix	Man page Source code
camera	Man page Source code
camera.default	Man page Source code
cameraPR	Man page Source code
cameraPR.default	Man page Source code
cbind	Man page
cbind.EList	Man page Source code
cbind.EListRaw	Man page
cbind.MAList	Man page Source code
cbind.RGList	Man page Source code
changeLog	Man page Source code
chooseLowessSpan	Man page Source code
classifyTestsF	Man page Source code
coerce,RGList,exprSet2-method	Man page
contrastAsCoef	Man page Source code
contrasts.fit	Man page Source code
controlStatus	Man page Source code
convest	Man page Source code
coolmap	Man page Source code
cumOverlap	Man page Source code
decideTests	Man page Source code
decideTests.MArrayLM	Man page Source code
decideTests.default	Man page Source code
designI2A	Man page Source code
designI2M	Man page Source code
detectionPValues	Man page Source code
detectionPValues.EListRaw	Man page Source code
detectionPValues.default	Man page Source code
diffSplice	Man page Source code
dim.EList	Man page Source code
dim.EListRaw	Man page
dim.MAList	Man page Source code
dim.MArrayLM	Man page Source code
dim.RGList	Man page Source code
dimnames.EList	Man page Source code
dimnames.EListRaw	Man page
dimnames.MAList	Man page Source code
dimnames.MArrayLM	Man page Source code
dimnames.RGList	Man page Source code
dimnames<-.EList	Man page
dimnames<-.EListRaw	Man page
dimnames<-.MAList	Man page
dimnames<-.RGList	Man page
duplicateCorrelation	Man page Source code
eBayes	Man page Source code
estimate.m0	Man page
exprs.MA	Man page Source code
fitFDist	Man page Source code
fitFDistRobustly	Man page Source code
fitGammaIntercept	Man page Source code
fitmixture	Man page Source code
fitted.MArrayLM	Man page Source code
fry	Man page Source code
fry.default	Man page Source code
genas	Man page Man page Source code
geneSetTest	Man page Source code
getDupSpacing	Man page Source code
getEAWP	Man page Source code
getGeneKEGGLinks	Man page Source code
getKEGGPathwayNames	Man page Source code
getLayout	Man page Source code
getLayout2	Man page Source code
getSpacing	Man page Source code
gls.series	Man page Source code
goana	Man page Source code
goana.MArrayLM	Man page Source code
goana.default	Man page Source code
gridc	Man page Source code
gridr	Man page Source code
head.EList	Man page
head.EListRaw	Man page
head.MAList	Man page
head.MArrayLM	Man page
head.RGList	Man page
head.TestResults	Man page
heatDiagram	Man page Source code
heatdiagram	Man page Source code
helpMethods	Man page Source code
ids2indices	Man page Source code
imageplot	Man page Source code
imageplot3by2	Man page Source code
interGeneCorrelation	Man page Source code
intraspotCorrelation	Man page Source code
is.fullrank	Man page Source code
isNumeric	Man page Source code
kegga	Man page Source code
kegga.MArrayLM	Man page Source code
kegga.default	Man page Source code
kooperberg	Man page
labels.TestResults	Man page Source code
levels.TestResults	Man page Source code
limma	Man page
limma-package	Man page
limmaUsersGuide	Man page Source code
lm.series	Man page Source code
lmFit	Man page Source code
lmscFit	Man page Source code
loessFit	Man page Source code
logcosh	Man page Source code
logsumexp	Man page Source code
ma3x3.matrix	Man page Source code
ma3x3.spottedarray	Man page Source code
makeContrasts	Man page Source code
makeUnique	Man page Source code
mdplot	Man page Source code
merge.EList	Man page Source code
merge.EListRaw	Man page Source code
merge.MAList	Man page Source code
merge.RGList	Man page Source code
mergeScans	Man page
mergeScansRG	Man page Source code
modelMatrix	Man page Source code
modifyWeights	Man page Source code
mrlm	Man page Source code
mroast	Man page Source code
mroast.default	Man page Source code
nec	Man page Source code
neqc	Man page Source code
nonEstimable	Man page Source code
normalizeBetweenArrays	Man page Source code
normalizeCyclicLoess	Man page Source code
normalizeForPrintorder	Man page Source code
normalizeForPrintorder.rg	Man page Source code
normalizeMedianAbsValues	Man page Source code
normalizeMedianValues	Man page Source code
normalizeQuantiles	Man page Source code
normalizeRobustSpline	Man page Source code
normalizeVSN	Man page Source code
normalizeVSN.EListRaw	Man page Source code
normalizeVSN.RGList	Man page Source code
normalizeVSN.default	Man page Source code
normalizeWithinArrays	Man page Source code
normexp.fit	Man page Source code
normexp.fit.control	Man page Source code
normexp.fit.detection.p	Man page Source code
normexp.signal	Man page Source code
plotDensities	Man page Source code
plotDensities.EList	Man page Source code
plotDensities.EListRaw	Man page Source code
plotDensities.MAList	Man page Source code
plotDensities.RGList	Man page Source code
plotDensities.default	Man page Source code
plotExonJunc	Man page Source code
plotExons	Man page Source code
plotFB	Man page Source code
plotFB.EListRaw	Man page Source code
plotFB.RGList	Man page Source code
plotFB.default	Man page Source code
plotMA	Man page Source code
plotMA.EList	Man page Source code
plotMA.EListRaw	Man page Source code
plotMA.MAList	Man page Source code
plotMA.MArrayLM	Man page Source code
plotMA.RGList	Man page Source code
plotMA.default	Man page Source code
plotMA3by2	Man page Source code
plotMD	Man page Source code
plotMD.EList	Man page Source code
plotMD.EListRaw	Man page Source code
plotMD.MAList	Man page Source code
plotMD.MArrayLM	Man page Source code
plotMD.RGList	Man page Source code
plotMD.default	Man page Source code
plotMDS	Man page Source code
plotMDS.MDS	Man page Source code
plotMDS.default	Man page Source code
plotPrintTipLoess	Man page Source code
plotPrintorder	Man page Source code
plotRLDF	Man page Source code
plotSA	Man page Source code
plotSplice	Man page Source code
plotWithHighlights	Man page Source code
plotlines	Man page Source code
poolVar	Man page Source code
predFCm	Man page Man page Source code
printHead	Man page Source code
printorder	Man page Source code
printtipWeights	Man page Source code
printtipWeightsSimple	Man page
propTrueNull	Man page Source code
propexpr	Man page Source code
protectMetachar	Man page Source code
qqf	Man page Source code
qqt	Man page Source code
rankSumTestWithCorrelation	Man page Source code
rbind.EList	Man page Source code
rbind.EListRaw	Man page
rbind.MAList	Man page Source code
rbind.RGList	Man page Source code
read.columns	Man page Source code
read.idat	Man page Source code
read.ilmn	Man page Source code
read.ilmn.targets	Man page Source code
read.imagene	Man page Source code
read.maimages	Man page Source code
readGAL	Man page Source code
readGPRHeader	Man page Source code
readGenericHeader	Man page Source code
readImaGeneHeader	Man page Source code
readSMDHeader	Man page Source code
readSpotTypes	Man page Source code
readTargets	Man page Source code
removeBatchEffect	Man page Source code
removeExt	Man page Source code
residuals.MArrayLM	Man page Source code
roast	Man page Source code
roast.default	Man page Source code
romer	Man page Source code
romer.default	Man page Source code
selectModel	Man page Source code
show,LargeDataObject-method	Man page
show,MDS-method	Man page
show,Roast-method	Man page
show,TestResults-method	Man page
spotc	Man page Source code
spotr	Man page Source code
squeezeVar	Man page Source code
strsplit2	Man page Source code
subsetListOfArrays	Man page Source code
subsetting	Man page
summary.EList	Man page Source code
summary.EListRaw	Man page
summary.MAList	Man page
summary.MArrayLM	Man page
summary.RGList	Man page
summary.TestResults	Man page Source code
tZscore	Man page Source code
tail.EList	Man page
tail.EListRaw	Man page
tail.MAList	Man page
tail.MArrayLM	Man page
tail.RGList	Man page
tail.TestResults	Man page
targetsA2C	Man page Source code
tmixture.matrix	Man page Source code
tmixture.vector	Man page Source code
topGO	Man page Source code
topKEGG	Man page Source code
topRomer	Man page Source code
topSplice	Man page Source code
topTable	Man page Source code
topTableF	Man page Source code
topTreat	Man page Source code
treat	Man page Source code
tricubeMovingAverage	Man page Source code
trigammaInverse	Man page Source code
trimWhiteSpace	Man page Source code
unique.TestResults	Man page Source code
uniqueTargets	Man page Source code
uniquegenelist	Man page Source code
unwrapdups	Man page Source code
vennCounts	Man page Source code
vennDiagram	Man page Source code
volcanoplot	Man page Source code
voom	Man page Source code
voomWithQualityWeights	Man page Source code
vooma	Man page Source code
voomaByGroup	Man page Source code
weighted.median	Man page
weightedLowess	Man page Source code
wilcoxGST	Man page Source code
write.fit	Man page Source code
wsva	Man page Source code
wtIgnore.Filter	Man page Source code
wtarea	Man page Source code
wtflags	Man page Source code
zscore	Man page Source code
zscoreGamma	Man page Source code
zscoreHyper	Man page Source code
zscoreT	Man page Source code