limma: Linear Models for Microarray Data

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]
Date of publication
None
Maintainer
Gordon Smyth <smyth@wehi.edu.au>
License
GPL (>=2)
Version
3.30.6
URLs

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

Files in this package

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