limma: Linear Models for Microarray Data

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("limma")
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)
Version3.30.13
http://bioinf.wehi.edu.au/limma

View on Bioconductor

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

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
alias2Symbol Man page
alias2SymbolTable Man page
alias2SymbolUsingNCBI Man page
anova.MAList Man page
array2channel Man page
arrayWeights Man page
arrayWeightsQuick Man page
arrayWeightsSimple Man page
as.data.frame.EList Man page
as.data.frame.EListRaw Man page
as.data.frame.MAList Man page
as.data.frame.MArrayLM Man page
as.MAList Man page
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
as.matrix.MArrayLM Man page
as.matrix.marrayNorm Man page
as.matrix.PLMset Man page
as.matrix.RGList Man page
as.matrix.vsn Man page
asMatrixWeights Man page
auROC Man page
avearrays Man page
avearrays.default Man page
avearrays.EList Man page
avearrays.MAList Man page
avedups Man page
avedups.default Man page
avedups.EList Man page
avedups.MAList Man page
avereps Man page
avereps.default Man page
avereps.EList Man page
avereps.EListRaw Man page
avereps.MAList Man page
avereps.RGList Man page
backgroundCorrect Man page
backgroundCorrect.matrix Man page
barcodeplot Man page
beadCountWeights Man page
blockDiag Man page
bwss Man page
bwss.matrix Man page
camera Man page
camera.default Man page
cbind Man page
cbind.EList Man page
cbind.EListRaw Man page
cbind.MAList Man page
cbind.RGList Man page
changeLog Man page
classifyTestsF Man page
classifyTestsP Man page
classifyTestsT Man page
coerce,RGList,exprSet2-method Man page
contrastAsCoef Man page
contrasts.fit Man page
controlStatus Man page
convest Man page
coolmap Man page
cumOverlap Man page
decideTests Man page
decideTests.default Man page
decideTests.MArrayLM Man page
designI2A Man page
designI2M Man page
detectionPValues Man page
detectionPValues.default Man page
detectionPValues.EListRaw Man page
diffSplice Man page
dim.EList Man page
dim.EListRaw Man page
dim.MAList Man page
dim.MArrayLM Man page
dimnames<-.EList Man page
dimnames.EList Man page
dimnames<-.EListRaw Man page
dimnames.EListRaw Man page
dimnames<-.MAList Man page
dimnames.MAList Man page
dimnames.MArrayLM Man page
dimnames<-.RGList Man page
dimnames.RGList Man page
dim.RGList Man page
duplicateCorrelation Man page
ebayes Man page
eBayes Man page
[.EList Man page
EList-class Man page
[.EListRaw Man page
EListRaw-class Man page
estimate.m0 Man page
exprs.MA Man page
fitFDist Man page
fitFDistRobustly Man page
fitGammaIntercept Man page
fitmixture Man page
fitted.MArrayLM Man page
fry Man page
fry.default Man page
FStat Man page
genas Man page
geneSetTest Man page
getDupSpacing Man page
getEAWP Man page
getGeneKEGGLinks Man page
getKEGGPathwayNames Man page
getLayout Man page
getLayout2 Man page
getSpacing Man page
gls.series Man page
goana Man page
goana.default Man page
goana.MArrayLM Man page
gridc Man page
gridr Man page
heatdiagram Man page
heatDiagram Man page
helpMethods Man page
ids2indices Man page
imageplot Man page
imageplot3by2 Man page
interGeneCorrelation Man page
intraspotCorrelation Man page
is.fullrank Man page
isNumeric Man page
kegga Man page
kegga.default Man page
kegga.MArrayLM Man page
kooperberg Man page
LargeDataObject-class Man page
length.EList Man page
length.EListRaw Man page
length.MAList Man page
length.MArrayLM Man page
length.RGList Man page
limma Man page
limma-package Man page
limmaUsersGuide Man page
lmFit Man page
lmscFit Man page
lm.series Man page
loessFit Man page
logcosh Man page
ma3x3.matrix Man page
ma3x3.spottedarray Man page
makeContrasts Man page
makeUnique Man page
[.MAList Man page
MAList-class Man page
MA.RG Man page
[.MArrayLM Man page
MArrayLM-class Man page
mdplot Man page
MDS-class Man page
merge.EList Man page
merge.EListRaw Man page
merge.MAList Man page
merge.RGList Man page
mergeScans Man page
mergeScansRG Man page
modelMatrix Man page
modifyWeights Man page
mrlm Man page
mroast Man page
mroast.default Man page
nec Man page
neqc Man page
nonEstimable Man page
normalizeBetweenArrays Man page
normalizeCyclicLoess Man page
normalizeForPrintorder Man page
normalizeForPrintorder.rg Man page
normalizeMedianAbsValues Man page
normalizeMedianValues Man page
normalizeQuantiles Man page
normalizeRobustSpline Man page
normalizeVSN Man page
normalizeVSN.default Man page
normalizeVSN.EListRaw Man page
normalizeVSN.RGList Man page
normalizeWithinArrays Man page
normexp.fit Man page
normexp.fit.control Man page
normexp.fit.detection.p Man page
normexp.signal Man page
plotDensities Man page
plotDensities.default Man page
plotDensities.EList Man page
plotDensities.EListRaw Man page
plotDensities.MAList Man page
plotDensities.RGList Man page
plotExons Man page
plotFB Man page
plotFB.default Man page
plotFB.EListRaw Man page
plotFB.RGList Man page
plotlines Man page
plotMA Man page
plotMA3by2 Man page
plotMA.default Man page
plotMA.EList Man page
plotMA.EListRaw Man page
plotMA.MAList Man page
plotMA.MArrayLM Man page
plotMA.RGList Man page
plotMD Man page
plotMD.default Man page
plotMD.EList Man page
plotMD.EListRaw Man page
plotMD.MAList Man page
plotMD.MArrayLM Man page
plotMD.RGList Man page
plotMDS Man page
plotMDS.default Man page
plotMDS.MDS Man page
plotPrintorder Man page
plotPrintTipLoess Man page
plotRLDF Man page
plotSA Man page
plotSplice Man page
plotWithHighlights Man page
poolVar Man page
predFCm Man page
printHead Man page
PrintLayout-class Man page
printorder Man page
printtipWeights Man page
printtipWeightsSimple Man page
propexpr Man page
propTrueNull Man page
protectMetachar Man page
qqf Man page
qqt Man page
QualityWeights Man page
rankSumTestWithCorrelation Man page
rbind.EList Man page
rbind.EListRaw Man page
rbind.MAList Man page
rbind.RGList Man page
read.columns Man page
readGAL Man page
readGenericHeader Man page
readGPRHeader Man page
read.idat Man page
read.ilmn Man page
read.ilmn.targets Man page
read.imagene Man page
readImaGeneHeader Man page
read.maimages Man page
readSMDHeader Man page
readSpotTypes Man page
readTargets Man page
removeBatchEffect Man page
removeExt Man page
residuals.MArrayLM Man page
[.RGList Man page
RGList-class Man page
RG.MA Man page
roast Man page
Roast-class Man page
roast.default Man page
romer Man page
romer.default Man page
selectModel Man page
show,LargeDataObject-method Man page
show,MDS-method Man page
show,Roast-method Man page
show,TestResults-method Man page
spotc Man page
spotr Man page
squeezeVar Man page
strsplit2 Man page
subsetListOfArrays Man page
subsetting Man page
summary.EList Man page
summary.EListRaw Man page
summary.MAList Man page
summary.MArrayLM Man page
summary.RGList Man page
summary.TestResults Man page
targetsA2C Man page
TestResults-class Man page
tmixture.matrix Man page
tmixture.vector Man page
topGO Man page
topKEGG Man page
topRomer Man page
topSplice Man page
toptable Man page
topTable Man page
topTableF Man page
topTreat Man page
treat Man page
tricubeMovingAverage Man page
trigammaInverse Man page
trimWhiteSpace Man page
tZscore Man page
uniquegenelist Man page
uniqueTargets Man page
unwrapdups Man page
vennCounts Man page
vennDiagram Man page
volcanoplot Man page
voom Man page
vooma Man page
voomaByGroup Man page
voomWithQualityWeights Man page
weightedLowess Man page
weighted.median Man page
wilcoxGST Man page
write.fit Man page
wtarea Man page
wtflags Man page
wtIgnore.Filter Man page
zscore Man page
zscoreGamma Man page
zscoreHyper Man page
zscoreT Man page

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-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/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/zscore.Rd
src
src/normexp.c
src/weighted_lowess.c
tests
tests/limma-Tests.R
tests/limma-Tests.Rout.save
vignettes
vignettes/intro.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.