Files in hdeberg/limma

Linear Models for Microarray Data

R/alias2Symbol.R R/arrayWeights.R R/arrayWeightsGeneByGene.R R/arrayWeightsPrWtsREML.R R/arrayWeightsQuick.R R/arrayWeightsREML.R R/auROC.R R/avearrays.R R/background-kooperberg.R R/background-normexp.R R/background.R R/barcodeplot.R R/beadCountWeights.R R/bwss.R R/chooseLowessSpan.R R/classes.R R/combine.R R/contrastAsCoef.R R/contrasts.R R/convest.R R/coolmap.R R/cumOverlap.R R/decidetests.R R/detectionPValues.R R/diffSplice.R R/dups.R R/ebayes.R R/fitFDist.R R/fitFDistRobustly.R R/fitGammaIntercept.R R/fitmixture.R R/genas.R R/geneset-camera.R R/geneset-cameraPR.R R/geneset-fry.R R/geneset-ids2indices.R R/geneset-roast.R R/geneset-romer.R R/geneset-wilcox.R R/goana.R R/kegga.R R/lmEffects.R R/lmfit.R R/loessFit.R R/logsumexp.R R/mergeScans.R R/modelmatrix.R R/neqc.R R/norm.R R/plotExonJunc.R R/plotExons.R R/plotFB.R R/plotMD.R R/plotMDS.R R/plotSplice.R R/plotWithHighlights.R R/plotdensities.R R/plotlines.R R/plotrldf.R R/plots-fit.R R/plots-image.R R/plots-ma.R R/poolvar.R R/predFCm.R R/printtipWeights.R R/propTrueNull.R R/propexpr.R R/qqt.R R/rankSumTestWithCorrelation.R R/read-ilmn.R R/read-imagene.R R/read-maimages.R R/read.R R/read.idat.R R/readHeader.R R/removeBatchEffect.R R/selmod.R R/sepchannel.R R/squeezeVar.R R/subsetting.R R/topSplice.R R/topTableF.R R/toptable.R R/treat.R R/tricubeMovingAverage.R R/utility.R R/venn.R R/voom.R R/voomWithQualityWeights.R R/vooma.R R/weightedLowess.R R/weightedmedian.R R/weights.R R/write.R R/wsva.R R/zscore.R R/zscoreHyper.R R/zzz.R inst/doc/usersguide.pdf man/01Introduction.Rd man/02classes.Rd man/03reading.Rd man/04Background.Rd man/05Normalization.Rd man/06linearmodels.Rd man/07SingleChannel.Rd man/08Tests.Rd man/09Diagnostics.Rd man/10GeneSetTests.Rd man/11RNAseq.Rd man/EList.Rd man/LargeDataObject.Rd man/PrintLayout.Rd man/TestResults.Rd man/alias2Symbol.Rd man/anova-method.Rd man/arrayWeights.Rd man/arrayWeightsQuick.Rd man/asMatrixWeights.Rd man/asdataframe.Rd man/asmalist.Rd man/asmatrix.Rd man/auROC.Rd man/avearrays.Rd man/avedups.Rd man/avereps.Rd man/backgroundcorrect.Rd man/barcodeplot.Rd man/beadCountWeights.Rd man/blockDiag.Rd man/bwss.Rd man/bwss.matrix.Rd man/camera.Rd man/cbind.Rd man/changelog.Rd man/channel2M.Rd man/chooseLowessSpan.Rd man/classifytestsF.Rd man/contrastAsCoef.Rd man/contrasts.fit.Rd man/controlStatus.Rd man/coolmap.Rd man/cumOverlap.Rd man/decideTests.Rd man/detectionPValue.Rd man/diffSplice.Rd man/dim.Rd man/dimnames.Rd man/dupcor.Rd man/ebayes.Rd man/exprsMA.Rd man/fitGammaIntercept.Rd man/fitfdist.Rd man/fitmixture.Rd man/fitted.MArrayLM.Rd man/genas.Rd man/geneSetTest.Rd man/getEAWP.Rd man/getSpacing.Rd man/getlayout.Rd man/gls.series.Rd man/goana.Rd man/gridspotrc.Rd man/head.Rd man/heatdiagram.Rd man/helpMethods.Rd man/ids2indices.Rd man/imageplot.Rd man/imageplot3by2.Rd man/intraspotCorrelation.Rd man/isfullrank.Rd man/isnumeric.Rd man/kooperberg.Rd man/limmaUsersGuide.Rd man/lm.series.Rd man/lmFit.Rd man/lmscFit.Rd man/loessfit.Rd man/logcosh.Rd man/logsumexp.Rd man/ma3x3.Rd man/makeContrasts.Rd man/makeunique.Rd man/malist.Rd man/marraylm.Rd man/mdplot.Rd man/merge.Rd man/mergeScansRG.Rd man/modelMatrix.Rd man/modifyWeights.Rd man/mrlm.Rd man/nec.Rd man/normalizeCyclicLoess.Rd man/normalizeMedianAbsValues.Rd man/normalizeRobustSpline.Rd man/normalizeVSN.Rd man/normalizeWithinArrays.Rd man/normalizebetweenarrays.Rd man/normalizeprintorder.Rd man/normalizequantiles.Rd man/normexpfit.Rd man/normexpfitcontrol.Rd man/normexpfitdetectionp.Rd man/normexpsignal.Rd man/plotDensities.Rd man/plotExonJunc.Rd man/plotExons.Rd man/plotFB.Rd man/plotMD.Rd man/plotMDS.Rd man/plotRLDF.Rd man/plotSA.Rd man/plotSplice.Rd man/plotWithHighlights.Rd man/plotlines.Rd man/plotma.Rd man/plotma3by2.Rd man/plotprinttiploess.Rd man/poolvar.Rd man/predFCm.Rd man/printHead.Rd man/printorder.Rd man/printtipWeights.Rd man/propTrueNull.Rd man/propexpr.Rd man/protectMetachar.Rd man/qqt.Rd man/qualwt.Rd man/rankSumTestwithCorrelation.Rd man/read.columns.Rd man/read.idat.Rd man/read.ilmn.Rd man/read.ilmn.targets.Rd man/read.maimages.Rd man/readGPRHeader.Rd man/readImaGeneHeader.Rd man/readSpotTypes.Rd man/readTargets.Rd man/readgal.Rd man/removeBatchEffect.Rd man/removeext.Rd man/residuals.MArrayLM.Rd man/rglist.Rd man/roast.Rd man/romer.Rd man/selectmodel.Rd man/squeezeVar.Rd man/strsplit2.Rd man/subsetting.Rd man/summary.Rd man/targetsA2C.Rd man/tmixture.Rd man/topGO.Rd man/topRomer.Rd man/topSplice.Rd man/toptable.Rd man/tricubeMovingAverage.Rd man/trigammainverse.Rd man/trimWhiteSpace.Rd man/uniquegenelist.Rd man/unwrapdups.Rd man/venn.Rd man/volcanoplot.Rd man/voom.Rd man/voomWithQualityWeights.Rd man/vooma.Rd man/weightedLowess.Rd man/weightedmedian.Rd man/writefit.Rd man/wsva.Rd man/zscore.Rd man/zscoreT.Rd tests/limma-Tests.R