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This is the development version of limma; for the stable release version, see limma.

Linear Models for Microarray Data

Bioconductor version: Development (3.3)

Data analysis, linear models and differential expression for microarray data.

Author: Gordon Smyth [cre,aut], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Natalie Thorne [ctb], Davis McCarthy [ctb], Di Wu [ctb], Yifang Hu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb], Aaron Lun [ctb]

Maintainer: Gordon Smyth <smyth at>

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PDF Limma One Page Introduction
PDF usersguide.pdf
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BatchEffect, Bayesian, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, GeneSetEnrichment, Genetics, Microarray, MultipleComparison, Normalization, OneChannel, Preprocessing, ProprietaryPlatforms, QualityControl, RNASeq, Regression, Software, TimeCourse, Transcription, TwoChannel, mRNAMicroarray, microRNAArray
Version 3.27.5
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License GPL (>=2)
Depends R (>= 2.3.0), methods
Imports grDevices, graphics, stats, utils
Suggests affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, illuminaio, KEGGREST, locfit, MASS,, splines, statmod (>= 1.2.2), vsn
Depends On Me a4Base, AffyExpress, AgiMicroRna, attract, birta, CALIB, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, coRNAi, DiffBind, DrugVsDisease, edgeR, ExiMiR, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, MLSeq, MmPalateMiRNA, prot2D, qpcrNorm, qusage, RBM, Ringo, RnBeads, Rnits, snapCGH, SSPA, tRanslatome, TurboNorm, wateRmelon
Imports Me ABSSeq, affycoretools, affylmGUI, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, ballgown, beadarray, BeadArrayUseCases, betr, birte, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, ChAMP, charm, ChIPComp, ChIPpeakAnno, compcodeR, csaw, DAPAR, derfinderPlot, diffHic, DmelSGI, DMRcate, EnrichmentBrowser, erccdashboard, explorase, flowBin, GeneSelectMMD, GeneSelector, GGBase, GOsummaries, gQTLstats, iCheck, iChip, InPAS, limmaGUI, lmdme, LVSmiRNA, mAPKL, maSigPro, MEAL, minfi, miRLAB, missMethyl, MmPalateMiRNA, monocle, MSstats, nem, nethet, nondetects, OGSA, OLIN, PAA, PADOG, PECA, pepStat, phenoTest, polyester, rCGH, ReportingTools, Ringo, RNAinteract, RTCGAToolbox, RTN, RTopper, SimBindProfiles, snapCGH, STATegRa, systemPipeR, TCGAbiolinks, timecourse, ToPASeq, tweeDEseq, variancePartition, vsn
Suggests Me ABarray, ADaCGH2, beadarraySNP, biobroom, BiocCaseStudies, BioNet, Category, categoryCompare, ClassifyR, CMA, coGPS, derfinder, dyebias, ELBOW, gage, GeneSelector, GEOquery, GSRI, GSVA, Heatplus, inSilicoDb, isobar, les, lumi, mammaPrintData, mdgsa, methylumi, MLP, npGSEA, oligo, oneChannelGUI, paxtoolsr, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, seventyGeneData, subSeq, sva
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