limma: Linear Models for Microarray Data
Version 3.32.2

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

AuthorGordon 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]
Bioconductor views AlternativeSplicing BatchEffect Bayesian Clustering DataImport DifferentialExpression DifferentialSplicing ExonArray GeneExpression GeneSetEnrichment Genetics Microarray MultipleComparison Normalization OneChannel Preprocessing ProprietaryPlatforms QualityControl RNASeq Regression TimeCourse Transcription TwoChannel mRNAMicroarray microRNAArray
Date of publicationNone
MaintainerGordon Smyth <smyth@wehi.edu.au>
LicenseGPL (>=2)
Version3.32.2
URL http://bioinf.wehi.edu.au/limma
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("limma")

Popular man pages

anova-method: ANOVA Table - method
heatdiagram: Stemmed Heat Diagram
limmaUsersGuide: View Limma User's Guide
read.idat: Read Illumina expression data directly from IDAT files
removeBatchEffect: Remove Batch Effect
venn: Venn Diagrams
volcanoplot: Volcano Plot
See all...

All man pages Function index File listing

Man pages

01Introduction: Introduction to the LIMMA Package
02classes: Topic: Classes Defined by this Package
03reading: Topic: Reading Microarray Data from Files
04Background: Topic: Background Correction
05Normalization: Topic: Normalization of Microarray Data
06linearmodels: Topic: Linear Models for Microarrays
07SingleChannel: Topic: Individual Channel Analysis of Two-Color Microarrays
08Tests: Topic: Hypothesis Testing for Linear Models
09Diagnostics: Topic: Diagnostics and Quality Assessment
10GeneSetTests: Topic: Gene Set Tests
11RNAseq: Topic: Analysis of RNA-seq Data
alias2Symbol: Convert Gene Aliases to Official Gene Symbols
anova-method: ANOVA Table - method
arrayWeights: Array Quality Weights
arrayWeightsQuick: Array Quality Weights
asdataframe: Turn a Microarray Linear Model Object into a Dataframe
asmalist: Convert marrayNorm Object to an MAList Object
asmatrix: Turn a Microarray Data Object into a Matrix
asMatrixWeights: asMatrixWeights
auROC: Area Under Receiver Operating Curve
avearrays: Average Over Replicate Arrays
avedups: Average Over Duplicate Spots
avereps: Average Over Irregular Replicate Probes
backgroundcorrect: Correct Intensities for Background
barcodeplot: Barcode Enrichment Plot
beadCountWeights: Bead Count Weights for Illumina BeadChips
blockDiag: Block Diagonal Matrix
bwss: Between and within sums of squares
bwss.matrix: Between and within sums of squares for matrix
camera: Competitive Gene Set Test Accounting for Inter-gene...
cbind: Combine RGList, MAList, EList or EListRaw Objects
changelog: Limma Change Log
channel2M: Convert Individual Channel Design Matrix to M-A Format
classifytests: Multiple Testing Genewise Across Contrasts
contrastAsCoef: Reform a Design Matrix to that Contrasts Become Coefficients
contrasts.fit: Compute Contrasts from Linear Model Fit
controlStatus: Set Status of each Spot from List of Spot Types
coolmap: Heatmap of gene expression values
cumOverlap: Cumulative Overlap Analysis of Ordered Lists
decideTests: Multiple Testing Across Genes and Contrasts
detectionPValue: Detection P-Values from Negative Controls
diffSplice: Test for Differential Splicing
dim: Retrieve the Dimensions of an RGList, MAList or MArrayLM...
dimnames: Retrieve the Dimension Names of an RGList, MAList, EList,...
dupcor: Correlation Between Duplicates
ebayes: Empirical Bayes Statistics for Differential Expression
EList: Expression List - class
exprsMA: Extract Log-Expression Matrix from MAList
fitfdist: Moment Estimation of Scaled F-Distribution
fitGammaIntercept: Fit Intercept to Vector of Gamma Distributed Variates
fitmixture: Fit Mixture Model by Non-Linear Least Squares
fitted.MArrayLM: Fitted Values Method for MArrayLM Fits
genas: Genuine Association of Gene Expression Profiles
geneSetTest: Mean-rank Gene Set Test
getEAWP: Extract Basic Data from Expression Data Objects
getlayout: Extract the Print Layout of an Array from the GAL File
getSpacing: Get Numerical Spacing
gls.series: Fit Linear Model to Microarray Data by Generalized Least...
goana: Gene Ontology or KEGG Pathway Analysis
gridspotrc: Row and Column Positions on Microarray
heatdiagram: Stemmed Heat Diagram
helpMethods: Prompt for Method Help Topics
ids2indices: Convert Gene Identifiers to Indices for Gene Sets
imageplot: Image Plot of Microarray Statistics
imageplot3by2: Write Imageplots to Files
intraspotCorrelation: Intra-Spot Correlation for Two Color Data
isfullrank: Check for Full Column Rank
isnumeric: Test for Numeric Argument
kooperberg: Kooperberg Model-Based Background Correction for GenePix data
LargeDataObject: Large Data Object - class
limmaUsersGuide: View Limma User's Guide
lmFit: Linear Model for Series of Arrays
lmscFit: Fit Linear Model to Individual Channels of Two-Color Data
lm.series: Fit Linear Model to Microrray Data by Ordinary Least Squares
loessfit: Univariate Lowess With Prior Weights
logcosh: Logarithm of cosh
ma3x3: Two dimensional Moving Averages with 3x3 Window
makeContrasts: Construct Matrix of Custom Contrasts
makeunique: Make Values of Character Vector Unique
malist: M-value, A-value Expression List - class
marraylm: Microarray Linear Model Fit - class
mdplot: Mean-Difference Plot
merge: Merge RGList or MAList Data Objects
mergeScansRG: Merge two scans of two-color arrays
modelMatrix: Construct Design Matrix
modifyWeights: Modify Matrix of Weights By Control Status of Rows
mrlm: Fit Linear Model to Microrray Data by Robust Regression
nec: NormExp Background Correction and Normalization Using Control...
normalizebetweenarrays: Normalize Between Arrays
normalizeCyclicLoess: Normalize Columns of a Matrix by Cyclic Loess
normalizeMedianAbsValues: Normalize Columns of a Matrix to have the Median Absolute...
normalizeprintorder: Print-Order Normalization
normalizequantiles: Normalize Columns of a Matrix to have the same Quantiles
normalizeRobustSpline: Normalize Single Microarray Using Shrunk Robust Splines
normalizeVSN: Variance Stabilizing Normalization (vsn)
normalizeWithinArrays: Normalize Within Arrays
normexpfit: Fit Normal+Exp Convolution Model to Observed Intensities
normexpfitcontrol: Normexp Model Parameter Estimation Aided by Negative Controls
normexpfitdetectionp: Estimate Normexp Model Parameter Using Negative Controls...
normexpsignal: Expected Signal Given Observed Foreground Under Normal+Exp...
plotDensities: Plot Expression Densities
plotExons: Plot exons of differentially expressed gene
plotFB: FB-Plot
plotlines: plotlines
plotma: MA-Plot of Expression Data
plotma3by2: Write MA-Plots to Files
plotMD: Mean-Difference Plot of Expression Data
plotMDS: Multidimensional scaling plot of distances between gene...
plotprinttiploess: MA Plots by Print-Tip Group
plotRLDF: Plot of regularized linear discriminant functions for...
plotSA: Sigma vs A plot for microarray linear model
plotSplice: Differential splicing plot
plotWithHighlights: Scatterplot With Highlighting of Special Points
poolvar: Pool Sample Variances with Unequal Variances
predFCm: Predictive log fold change for microarrays
printHead: Print Leading Rows of Large Objects
PrintLayout: Print Layout - class
printorder: Identify Order in which Spots were Printed
printtipWeights: Sub-array Quality Weights
propexpr: Estimate Proportion of Expressed Probes
propTrueNull: Estimate Proportion of True Null Hypotheses
protectMetachar: Protect Metacharacters
qqt: Student's t Quantile-Quantile Plot
qualwt: Spot Quality Weights
rankSumTestwithCorrelation: Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For...
read.columns: Read specified columns from a file
readgal: Read a GAL file
readGPRHeader: Read Header Information from Microarray Raw Data File
read.idat: Read Illumina expression data directly from IDAT files
read.ilmn: Read Illumina Expression Data
read.ilmn.targets: Read Illumina Data from a Target Dataframe
readImaGeneHeader: Read ImaGene Header Information
read.maimages: Read RGList or EListRaw from Image Analysis Output Files
readSpotTypes: Read Spot Types File
readTargets: Read Targets File
removeBatchEffect: Remove Batch Effect
removeext: Remove Common Extension from File Names
residuals.MArrayLM: Extract Residuals from MArrayLM Fit
rglist: Red, Green Intensity List - class
roast: Rotation Gene Set Tests
romer: Rotation Gene Set Enrichment Analysis
selectmodel: Select Appropriate Linear Model
squeezeVar: Squeeze Sample Variances
strsplit2: Split Composite Names
subsetting: Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
summary: Summaries of Microarray Data Objects
targetsA2C: Convert Two-Color Targets Dataframe from One-Row-Per-Array to...
TestResults: Matrix of Test Results - class
tmixture: Estimate Scale Factor in Mixture of t-Distributions
topGO: Table of Top GO Terms or Top KEGG Pathways
topRomer: Top Gene Set Testing Results from Romer
topSplice: Top table of differentially spliced genes or exons
toptable: Table of Top Genes from Linear Model Fit
tricubeMovingAverage: Moving Average Smoother With Tricube Weights
trigammainverse: Inverse Trigamma Function
trimWhiteSpace: Trim Leading and Trailing White Space
uniquegenelist: Eliminate Duplicate Names from the Gene List
unwrapdups: Unwrap Duplicate Spot Values from Rows into Columns
venn: Venn Diagrams
volcanoplot: Volcano Plot
voom: Transform RNA-Seq Data Ready for Linear Modelling
vooma: Convert Mean-Variance Trend to Observation-specific Precision...
voomWithQualityWeights: Combining observational-level with sample-specific quality...
weightedLowess: Lowess fit with weighting
weightedmedian: Weighted Median
writefit: Write MArrayLM Object to a File
wsva: Weighted Surrogate Variable Analysis
zscore: Z-score Equivalents

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
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
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
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
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
zscore Man page Source code
zscoreGamma Man page Source code
zscoreHyper Man page Source code
zscoreT Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/alias2Symbol.R
R/arrayWeights.R
R/arrayWeightsSimple.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/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/mergeScans.R
R/modelmatrix.R
R/neqc.R
R/norm.R
R/plotExons.R
R/plotFB.R
R/plotMD.R
R/plotMDS.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/toptable.R
R/treat.R
R/tricubeMovingAverage.R
R/utility.R
R/venn.R
R/voom.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
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/changelog.txt
inst/doc/index.html
inst/doc/intro.Rnw
inst/doc/intro.pdf
inst/doc/usersguide.pdf
man
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/classifytests.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/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/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/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
src
src/init.c
src/normexp.c
src/weighted_lowess.c
tests
tests/limma-Tests.R
tests/limma-Tests.Rout.save
vignettes
vignettes/intro.Rnw
limma documentation built on May 20, 2017, 9:32 p.m.

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