To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("limma")

In most cases, you don't need to download the package archive at all.

limma

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data

Bioconductor version: 3.4

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

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

Maintainer: Gordon Smyth <smyth at wehi.edu.au>

Citation (from within R, enter citation("limma")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("limma")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("limma")

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

Details

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	3.30.13
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 12 years)
License	GPL (>=2)
Depends	R (>= 2.3.0)
Imports	grDevices, graphics, stats, utils, methods
LinkingTo
Suggests	affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn
SystemRequirements
Enhances
URL	http://bioinf.wehi.edu.au/limma
Depends On Me	a4Base, AffyExpress, AgiMicroRna, birta, bsseq, CALIB, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, coRNAi, DrugVsDisease, edgeR, ExiMiR, ExpressionAtlas, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, HTqPCR, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, MLSeq, MmPalateMiRNA, PGPC, prot2D, qpcrNorm, qusage, RBM, Ringo, RnBeads, Rnits, snapCGH, splineTimeR, SRGnet, SSPA, tRanslatome, TurboNorm, wateRmelon
Imports Me	ABSSeq, affycoretools, affylmGUI, anamiR, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, ballgown, BatchQC, beadarray, BeadArrayUseCases, betr, birte, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, CancerSubtypes, casper, ChAMP, charm, ChIPComp, ChIPpeakAnno, clusterExperiment, compcodeR, CONFESS, CountClust, crlmm, crossmeta, csaw, ctsGE, DAPAR, debrowser, derfinderPlot, DEsubs, DiffBind, diffHic, diffloop, DmelSGI, DMRcate, EBSEA, eegc, EGAD, EGSEA, EnrichmentBrowser, erccdashboard, explorase, flowBin, gCrisprTools, GeneSelectMMD, GeneSelector, GGBase, GOsummaries, gQTLstats, GUIDEseq, HTqPCR, iCheck, iChip, iCOBRA, InPAS, limmaGUI, Linnorm, lmdme, LVSmiRNA, mAPKL, MEAL, methylKit, MethylMix, minfi, miRLAB, missMethyl, MmPalateMiRNA, monocle, MoonlightR, MSstats, nem, nethet, nondetects, OGSA, OLIN, PAA, PADOG, PathoStat, pbcmc, pcaExplorer, PECA, pepStat, phenoTest, polyester, qsea, rCGH, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, RTCGAToolbox, RTN, RTopper, scater, sigaR, SimBindProfiles, snapCGH, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, timecourse, ToPASeq, TPP, tweeDEseq, variancePartition, vsn, yamss, yarn
Suggests Me	ABarray, ADaCGH2, beadarraySNP, biobroom, BiocCaseStudies, BioNet, Category, categoryCompare, ClassifyR, CMA, coGPS, derfinder, dyebias, ELBOW, gage, GeneSelector, GEOquery, GeuvadisTranscriptExpr, Glimma, GSRI, GSVA, Harman, Heatplus, isobar, les, lumi, mammaPrintData, MAST, mdgsa, methylumi, MLP, npGSEA, oligo, oneChannelGUI, oppar, paxtoolsr, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, scran, seventyGeneData, subSeq, sva, tximport
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	limma_3.30.13.tar.gz
Windows Binary	limma_3.30.13.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks)	limma_3.30.13.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/limma/tree/release-3.4
Package Short Url	http://bioconductor.org/packages/limma/
Package Downloads Report	Download Stats