limma: Linear Models for Microarray Data

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]
Date of publicationNone
MaintainerGordon Smyth <smyth@wehi.edu.au>
LicenseGPL (>=2)
Version3.30.8
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

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

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