Package: limma 3.63.3

Gordon Smyth

limma: Linear Models for Microarray and Omics Data

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

Authors: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], Goknur Giner [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb], Charity Law [ctb], Mengbo Li [ctb], Lizhong Chen [ctb]

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NEWS

# Install 'limma' in R:
install.packages('limma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:limma-3.63.3(bioc 3.21)limma-3.62.2(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics

13.79 score 585 packages 15k scripts 60k downloads 7.8k mentions 314 exports 1 dependencies

Last updated 1 months agofrom:97a5846be5. Checks:1 OK, 8 NOTE, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 09 2025
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R-4.4-win-x86_64NOTEFeb 09 2025
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Exports:[.EList[.EListRaw[.MAList[.MArrayLM[.RGList[.TestResultsalias2Symbolalias2SymbolTablealias2SymbolUsingNCBIanova.MAListarrayWeightsarrayWeightsQuickas.data.frame.EListas.data.frame.EListRawas.data.frame.MAListas.data.frame.MArrayLMas.MAListas.matrix.EListas.matrix.EListRawas.matrix.ExpressionSetas.matrix.LumiBatchas.matrix.MAListas.matrix.MArrayLMas.matrix.marrayNormas.matrix.PLMsetas.matrix.RGListas.matrix.vsnasMatrixWeightsauROCavearraysavearrays.defaultavearrays.EListavearrays.MAListavedupsavedups.defaultavedups.EListavedups.MAListaverepsavereps.defaultavereps.EListavereps.EListRawavereps.MAListavereps.RGListbackgroundCorrectbackgroundCorrect.matrixbarcodeplotbeadCountWeightsblockDiagbwssbwss.matrixcameracamera.defaultcameraPRcameraPR.defaultcbind.EListcbind.EListRawcbind.MAListcbind.RGListchangeLogchooseLowessSpanclassifyTestsFcontrastAsCoefcontrasts.fitcontrolStatusconvestcoolmapcumOverlapdecideTestsdecideTests.defaultdecideTests.MArrayLMdesignI2AdesignI2MdetectionPValuesdetectionPValues.defaultdetectionPValues.EListRawdiffSplicedim.EListdim.EListRawdim.MAListdim.MArrayLMdim.RGListdimnames.EListdimnames.EListRawdimnames.MAListdimnames.MArrayLMdimnames.RGListdimnames<-.EListdimnames<-.EListRawdimnames<-.MAListdimnames<-.RGListduplicateCorrelationeBayesexprs.MAfitFDistfitFDistRobustlyfitFDistUnequalDF1fitGammaInterceptfitmixturefitted.MArrayLMfryfry.defaultgenasgeneSetTestgetDupSpacinggetEAWPgetGeneKEGGLinksgetKEGGPathwayNamesgetLayoutgetLayout2getSpacinggls.seriesgoanagoana.defaultgoana.MArrayLMgoanaTrendgridcgridrhead.EListhead.EListRawhead.MAListhead.MArrayLMhead.RGListhead.TestResultsheatdiagramheatDiagramhelpMethodsids2indicesimageplotimageplot3by2interGeneCorrelationintraspotCorrelationis.fullrankisNumerickeggakegga.defaultkegga.MArrayLMkooperberglabels.TestResultslevels.TestResultslimmaUsersGuidelm.serieslmFitlmscFitloessFitlogcoshlogsumexpMA.RGma3x3.matrixma3x3.spottedarraymakeContrastsmakeUniquemdplotmerge.EListmerge.EListRawmerge.MAListmerge.RGListmergeScansRGmodelMatrixmodifyWeightsmrlmmroastmroast.defaultnecneqcnonEstimablenormalizeBetweenArraysnormalizeCyclicLoessnormalizeForPrintordernormalizeForPrintorder.rgnormalizeMedianAbsValuesnormalizeMedianValuesnormalizeQuantilesnormalizeRobustSplinenormalizeVSNnormalizeVSN.defaultnormalizeVSN.EListRawnormalizeVSN.RGListnormalizeWithinArraysnormexp.fitnormexp.fit.controlnormexp.fit.detection.pnormexp.signalplotDensitiesplotDensities.defaultplotDensities.EListplotDensities.EListRawplotDensities.MAListplotDensities.RGListplotExonJuncplotExonsplotFBplotFB.defaultplotFB.EListRawplotFB.RGListplotlinesplotMAplotMA.defaultplotMA.EListplotMA.EListRawplotMA.MAListplotMA.MArrayLMplotMA.RGListplotMA3by2plotMDplotMD.defaultplotMD.EListplotMD.EListRawplotMD.MAListplotMD.MArrayLMplotMD.RGListplotMDSplotMDS.defaultplotMDS.MDSplotPrintorderplotPrintTipLoessplotRLDFplotSAplotSpliceplotWithHighlightspoolVarpredFCmprintHeadprintorderprinttipWeightspropexprpropTrueNullprotectMetacharqqfqqtrankSumTestWithCorrelationrbind.EListrbind.EListRawrbind.MAListrbind.RGListread.columnsread.idatread.ilmnread.ilmn.targetsread.imageneread.maimagesreadGALreadGenericHeaderreadGPRHeaderreadImaGeneHeaderreadSMDHeaderreadSpotTypesreadTargetsremoveBatchEffectremoveExtresiduals.MArrayLMRG.MAroastroast.defaultromerromer.defaultsampleInfoFromGEOselectModelshowspotcspotrsqueezeVarstrsplit2subsetListOfArrayssummary.EListsummary.EListRawsummary.MAListsummary.MArrayLMsummary.RGListsummary.TestResultstail.EListtail.EListRawtail.MAListtail.MArrayLMtail.RGListtail.TestResultstargetsA2Ctmixture.matrixtmixture.vectortopGOtopKEGGtopRomertopSplicetopTabletopTableFtopTreattreattricubeMovingAveragetrigammaInversetrimWhiteSpacetZscoreunique.TestResultsuniquegenelistuniqueTargetsunwrapdupsvennCountsvennDiagramvolcanoplotvoomvoomavoomaByGroupvoomaLmFitvoomWithQualityWeightsweighted.medianweightedLowesswilcoxGSTwrite.fitwsvawtareawtflagswtIgnore.FilterzscorezscoreGammazscoreHyperzscoreT

Dependencies:statmod

A brief introduction to limma

Rendered fromintro.Rmdusingknitr::rmarkdownon Feb 09 2025.

Last update: 2023-06-11
Started: 2023-06-10

limma User's Guide

Rendered fromusersguide.Rnwusingutils::Sweaveon Feb 09 2025.

Last update: 2023-06-18
Started: 2023-06-18

Readme and manuals

Help Manual

Help pageTopics
Introduction to the LIMMA Packagelimma-package 01.Introduction limma
Topic: Classes Defined by this Package02.Classes
Topic: Reading Microarray Data from Files03.ReadingData
Topic: Background Correction04.Background
Topic: Normalization of Microarray Data05.Normalization
Topic: Linear Models for Microarrays06.LinearModels
Topic: Individual Channel Analysis of Two-Color Microarrays07.SingleChannel
Topic: Hypothesis Testing for Linear Models08.Tests
Topic: Diagnostics and Quality Assessment09.Diagnostics
Topic: Gene Set Tests10.GeneSetTests
Topic: Analysis of RNA-seq Data11.RNAseq
Convert Gene Aliases to Official Gene Symbolsalias2Symbol alias2SymbolTable alias2SymbolUsingNCBI
ANOVA Table - methodanova.MAList
Array Quality WeightsarrayWeights
Array Quality WeightsarrayWeightsQuick
Turn a Microarray Linear Model Object into a Dataframeas.data.frame.EList as.data.frame.EListRaw as.data.frame.MAList as.data.frame.MArrayLM
Convert marrayNorm Object to an MAList Objectas.MAList
Turn a Microarray Data Object into a Matrixas.matrix.EList as.matrix.EListRaw as.matrix.ExpressionSet as.matrix.LumiBatch as.matrix.MAList as.matrix.MArrayLM as.matrix.marrayNorm as.matrix.PLMset as.matrix.RGList as.matrix.vsn
asMatrixWeightsasMatrixWeights
Area Under Receiver Operating CurveauROC
Average Over Replicate Arraysavearrays avearrays.default avearrays.EList avearrays.MAList
Average Over Duplicate Spotsavedups avedups.default avedups.EList avedups.MAList
Average Over Irregular Replicate Probesavereps avereps.default avereps.EList avereps.EListRaw avereps.MAList avereps.RGList
Correct Intensities for BackgroundbackgroundCorrect backgroundCorrect.matrix
Barcode Enrichment Plotbarcodeplot
Bead Count Weights for Illumina BeadChipsbeadCountWeights
Block Diagonal MatrixblockDiag
Between and within sums of squaresbwss
Between and within sums of squares for matrixbwss.matrix
Competitive Gene Set Test Accounting for Inter-gene Correlationcamera camera.default cameraPR cameraPR.default interGeneCorrelation
Combine RGList, MAList, EList or EListRaw Objectscbind cbind.EList cbind.EListRaw cbind.MAList cbind.RGList rbind.EList rbind.EListRaw rbind.MAList rbind.RGList
Change LogchangeLog
Choose Span for Local-Weighted Regression SmoothingchooseLowessSpan
Genewise Nested F-TestsclassifyTestsF
Reform a Design Matrix to that Contrasts Become CoefficientscontrastAsCoef
Compute Contrasts from Linear Model Fitcontrasts.fit
Set Status of each Spot from List of Spot TypescontrolStatus
Heatmap of gene expression valuescoolmap
Cumulative Overlap Analysis of Ordered ListscumOverlap
Multiple Testing Across Genes and ContrastsdecideTests decideTests.default decideTests.MArrayLM
Convert Individual Channel Design Matrix to M-A FormatdesignI2A designI2M
Detection P-Values from Negative ControlsdetectionPValues detectionPValues.default detectionPValues.EListRaw
Test for Differential SplicingdiffSplice
Retrieve the Dimensions of an RGList, MAList or MArrayLM Objectdim.EList dim.EListRaw dim.MAList dim.MArrayLM dim.RGList
Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Objectdimnames.EList dimnames.EListRaw dimnames.MAList dimnames.MArrayLM dimnames.RGList dimnames<-.EList dimnames<-.EListRaw dimnames<-.MAList dimnames<-.RGList
Correlation Between Duplicates or Within BlocksduplicateCorrelation
Empirical Bayes Statistics for Differential ExpressioneBayes treat
Expression List (EList) classEList-class EListRaw-class
Extract Log-Expression Matrix from MAListexprs.MA
Moment Estimation of Scaled F-DistributionfitFDist fitFDistRobustly fitFDistUnequalDF1
Fit Intercept to Vector of Gamma Distributed VariatesfitGammaIntercept
Fit Mixture Model by Non-Linear Least Squaresfitmixture
Fitted Values Method for MArrayLM Fitsfitted.MArrayLM
Genuine Association of Gene Expression Profilesgenas
Mean-rank Gene Set TestgeneSetTest wilcoxGST
Extract Basic Data from Expression Data ObjectsgetEAWP
Extract the Print Layout of an Array from the GAL FilegetDupSpacing getLayout getLayout2
Get Numerical SpacinggetSpacing
Fit Linear Model to Microarray Data by Generalized Least Squaresgls.series
Gene Ontology or KEGG Pathway AnalysisgetGeneKEGGLinks getKEGGPathwayNames goana goana.default goana.MArrayLM kegga kegga.default kegga.MArrayLM
Estimate DE Trend for Gene Ontology or KEGG Pathway AnalysisgoanaTrend
Row and Column Positions on Microarraygridc gridr spotc spotr
Return the First to Last Part of a Data Objecthead.EList head.EListRaw head.MAList head.MArrayLM head.RGList head.TestResults tail.EList tail.EListRaw tail.MAList tail.MArrayLM tail.RGList tail.TestResults
Stemmed Heat DiagramheatDiagram heatdiagram
Prompt for Method Help TopicshelpMethods
Convert Gene Identifiers to Indices for Gene Setsids2indices
Image Plot of Microarray Statisticsimageplot
Write Imageplots to Filesimageplot3by2
Intra-Spot Correlation for Two Color DataintraspotCorrelation
Check for Full Column Rankis.fullrank nonEstimable
Test for Numeric ArgumentisNumeric
Kooperberg Model-Based Background Correction for GenePix datakooperberg
Large Data Object - classLargeDataObject-class show,LargeDataObject-method
View Limma User's GuidelimmaUsersGuide
Fit Linear Model to Microrray Data by Ordinary Least Squareslm.series
Linear Model for Series of ArrayslmFit
Fit Linear Model to Individual Channels of Two-Color DatalmscFit
Univariate Lowess With Prior WeightsloessFit
Logarithm of coshlogcosh
Log Sum of Exponentialslogsumexp
Two dimensional Moving Averages with 3x3 Windowma3x3.matrix ma3x3.spottedarray
Construct Matrix of Custom ContrastsmakeContrasts
Make Values of Character Vector UniquemakeUnique
M-value, A-value Expression List - classMAList-class
Microarray Linear Model Fit - classMArrayLM-class
Mean-Difference Plotmdplot
Merge RGList or MAList Data Objectsmerge.EList merge.EListRaw merge.MAList merge.RGList
Merge two scans of two-color arraysmergeScans mergeScansRG
Construct Design MatrixmodelMatrix uniqueTargets
Modify Matrix of Weights By Control Status of RowsmodifyWeights
Fit Linear Model to Microrray Data by Robust Regressionmrlm
NormExp Background Correction and Normalization Using Control Probesnec neqc
Normalize Between ArraysnormalizeBetweenArrays
Normalize Columns of a Matrix by Cyclic LoessnormalizeCyclicLoess
Print-Order NormalizationnormalizeForPrintorder normalizeForPrintorder.rg plotPrintorder
Normalize Columns of a Matrix to have the Median Absolute ValuenormalizeMedianAbsValues normalizeMedianValues
Normalize Columns of a Matrix to have the same QuantilesnormalizeQuantiles
Normalize Single Microarray Using Shrunk Robust SplinesnormalizeRobustSpline
Variance Stabilizing Normalization (vsn)normalizeVSN normalizeVSN.default normalizeVSN.EListRaw normalizeVSN.RGList
Normalize Within ArraysMA.RG normalizeWithinArrays RG.MA
Fit Normal+Exp Convolution Model to Observed Intensitiesnormexp.fit
Normexp Model Parameter Estimation Aided by Negative Controlsnormexp.fit.control
Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probesnormexp.fit.detection.p
Expected Signal Given Observed Foreground Under Normal+Exp Modelnormexp.signal
Plot Expression DensitiesplotDensities plotDensities.default plotDensities.EList plotDensities.EListRaw plotDensities.MAList plotDensities.RGList
Differential splicing plot with junctionsplotExonJunc
Plot exons of differentially expressed geneplotExons
FB-PlotplotFB plotFB.default plotFB.EListRaw plotFB.RGList
plotlinesplotlines
MA-Plot of Expression DataplotMA plotMA.default plotMA.EList plotMA.EListRaw plotMA.MAList plotMA.MArrayLM plotMA.RGList
Write MA-Plots to FilesplotMA3by2
Mean-Difference Plot of Expression DataplotMD plotMD.default plotMD.EList plotMD.EListRaw plotMD.MAList plotMD.MArrayLM plotMD.RGList
Multidimensional scaling plot of distances between gene expression profilesMDS-class plotMDS plotMDS.default plotMDS.MDS show,MDS-method
MA Plots by Print-Tip GroupplotPrintTipLoess
Plot of regularized linear discriminant functions for microarray dataplotRLDF
Sigma vs A plot for microarray linear modelplotSA
Differential splicing plotplotSplice
Scatterplot With Highlighting of Special PointsplotWithHighlights
Pool Sample Variances with Unequal VariancespoolVar
Predictive log fold change for microarrayspredFCm
Print Leading Rows of Large ObjectsprintHead
Print Layout - classPrintLayout-class
Identify Order in which Spots were Printedprintorder
Sub-array Quality WeightsprinttipWeights printtipWeightsSimple
Estimate Proportion of Expressed Probespropexpr
Estimate Proportion of True Null Hypothesesconvest estimate.m0 propTrueNull
Protect MetacharactersprotectMetachar
Student's t or Fisher's F Quantile-Quantile Plotqqf qqt
Spot Quality Weights for Spotted MicroarraysQualityWeights wtarea wtflags wtIgnore.Filter
Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For CorrelationrankSumTestWithCorrelation
Read specified columns from a fileread.columns
Read Illumina expression data from IDAT filesread.idat
Read Illumina Expression Dataread.ilmn
Read Illumina Data from a Target Dataframeread.ilmn.targets
Read RGList or EListRaw from Image Analysis Output Filesread.imagene read.maimages
Read a GAL filereadGAL
Read Header Information from Microarray Raw Data FilereadGenericHeader readGPRHeader readSMDHeader
Read ImaGene Header InformationreadImaGeneHeader
Read Spot Types FilereadSpotTypes
Read Targets FilereadTargets
Remove Batch EffectremoveBatchEffect
Remove Common Extension from File NamesremoveExt
Extract Residuals from MArrayLM Fitresiduals.MArrayLM
Red, Green Intensity List - classcoerce,RGList,exprSet2-method RGList-class
Rotation Gene Set Testsfry fry.default mroast mroast.default roast Roast-class roast.default show,Roast-method
Rotation Gene Set Enrichment Analysisromer romer.default
Read Sample Characteristics From GEO Series Matrix FilesampleInfoFromGEO
Select Appropriate Linear ModelselectModel
Squeeze Sample VariancessqueezeVar
Split Composite Namesstrsplit2
Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults ObjectssubsetListOfArrays subsetting [.EList [.EListRaw [.MAList [.MArrayLM [.RGList [.TestResults
Summaries of Microarray Data Objectssummary.EList summary.EListRaw summary.MAList summary.MArrayLM summary.RGList
Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channelarray2channel targetsA2C
Matrix of Test Results - classlabels.TestResults levels.TestResults show,TestResults-method summary.TestResults TestResults-class unique.TestResults
Estimate Scale Factor in Mixture of t-Distributionstmixture.matrix tmixture.vector
Table of Top GO Terms or Top KEGG PathwaystopGO topKEGG
Top Gene Set Testing Results from RomertopRomer
Top table of differentially spliced genes or exonstopSplice
Table of Top Genes from Linear Model FittopTable topTableF topTreat
Moving Average Smoother With Tricube WeightstricubeMovingAverage
Inverse Trigamma FunctiontrigammaInverse
Trim Leading and Trailing White SpacetrimWhiteSpace
Eliminate Duplicate Names from the Gene Listuniquegenelist
Unwrap Duplicate Spot Values from Rows into Columnsunwrapdups
Venn DiagramsvennCounts vennDiagram
Volcano Plotvolcanoplot
Transform RNA-Seq Counts for Linear Modeling With Precision Weightsvoom
Convert Variance Trend to Observation Precision Weights for Microarray-style Datavooma voomaByGroup
Apply vooma-lmFit Pipeline With Automatic Estimation of Sample Weights and Block CorrelationvoomaLmFit
Transform RNA-Seq Counts for Linear Modeling With Precision and Sample WeightsvoomWithQualityWeights
Weighted Medianweighted.median
LOWESS Smoother with Prior WeightsweightedLowess
Write MArrayLM Object to a Filewrite.fit
Weighted Surrogate Variable Analysiswsva
Transform non-normal random deviates to standard normalzscore zscoreGamma zscoreHyper
Transform t-statistics to standard normaltZscore zscoreT