API for limma
Linear Models for Microarray Data

Global functions
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
FStat Man page Source code
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
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
arrayWeightsSimple Man page Source code
as.MAList Man page Source code
as.data.frame.EList Man page
as.data.frame.EListRaw Man page
as.data.frame.MAList Man page Source code
as.data.frame.MArrayLM Man page Source code
as.matrix.EList Man page
as.matrix.EListRaw Man page
as.matrix.ExpressionSet Man page
as.matrix.LumiBatch Man page
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 Source code
bayesianAdjustedFG Source code
beadCountWeights Man page Source code
bg.parameters.rma75 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
cbind.EListRaw Man page
cbind.MAList Man page Source code
cbind.RGList Man page Source code
changeLog Man page Source code
classifyTestsF Man page Source code
classifyTestsP Man page Source code
classifyTestsT 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
denominatorBayesianAdjustedFG 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
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
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
ebayes Man page Source code Source code
estimate.m0 Man page
expectedBayesianAdjustedFG Source code
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
fryEffects 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
getas 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
heatDiagram Man page Source code
heatdiagram Man page Source code
helpMethods Man page Source code
hockey 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 Source code
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
lmEffects Source code
lmFit Man page Source code
lmn.biological.variance 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
matvec Source code
mdplot Man page Source code
meanHalf 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
mergeScans1 Source code
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
multTLogLik Source code
multTLogLikNull Source code
nec Man page Source code
neqc Man page Source code
nonEstimable Man page Source code
normalConvolution 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.gm2loglik Source code
normexp.hm2loglik Source code
normexp.m2loglik Source code
normexp.signal Man page Source code
numeratorBayesianAdjustedFG Source code
onAttach Source code
onLoad Source code
onUnload 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
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
propTrueNullByLocalFDR Source code
propTrueNullByMeanP Source code
propTrueNullFromHistogram 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
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
read.oneilmnfile 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
roastEffects Source code
romer Man page Source code
romer.default Man page Source code
selectModel Man page Source code
setdimnames 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 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
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
topTableT Source code
topTreat Man page Source code
toptable Man page Source code
treat Man page Source code
tricubeMovingAverage Man page Source code
trigammaInverse Man page Source code
trimWhiteSpace Man page Source code
uniqueTargets Man page Source code
uniquegenelist Man page Source code
unwrapdups Man page Source code
varaux1 Source code
varaux2 Source code
vecmat 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 Source code
weightedLowess Man page Source code
whichGenes 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
zeroDominantMatrixMult Source code
zscore Man page Source code
zscoreGamma Man page Source code
zscoreHyper Man page Source code
zscoreT Man page Source code
limma documentation built on June 22, 2018, 6 p.m.