{ "_id": "6ae7d0032e87f76f20ace00f", "Package": "limma", "Version": "3.99.4", "Date": "2026-11-01", "Title": "Linear Models for Microarray and Omics Data", "Description": "Data analysis, linear models and differential expression\nfor omics data.", "Authors@R": "c(person(given = \"Gordon\",\nfamily = \"Smyth\",\nrole = c(\"cre\", \"aut\"),\nemail = \"smyth@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0001-9221-2892\")),\nperson(given = \"Lizhong\",\nfamily = \"Chen\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-8326-6781\")),\nperson(given = \"Matthew\",\nfamily = \"Ritchie\",\nrole = \"ctb\"),\nperson(given = \"Belinda\",\nfamily = \"Phipson\",\nrole = \"ctb\"),\nperson(given = \"Di\",\nfamily = \"Wu\",\nrole = \"ctb\"),\nperson(given = \"Yifang\",\nfamily = \"Hu\",\nrole = \"ctb\"),\nperson(given = \"Charity\",\nfamily = \"Law\",\nrole = \"ctb\"),\nperson(given = \"Wei\",\nfamily = \"Shi\",\nrole = \"ctb\"),\nperson(given = \"James\",\nfamily = \"Wettenhall\",\nrole = \"ctb\"),\nperson(given = \"Yunshun\",\nfamily = \"Chen\",\nrole = \"ctb\"),\nperson(given = \"Mengbo\",\nfamily = \"Li\",\nrole = \"ctb\"),\nperson(given = \"Jeremy\",\nfamily = \"Silver\",\nrole = \"ctb\"),\nperson(given = \"Aaron\",\nfamily = \"Lun\",\nrole = \"ctb\"),\nperson(given = \"Davis\",\nfamily = \"McCarthy\",\nrole = \"ctb\"),\nperson(given = \"Natalie\",\nfamily = \"Thorne\",\nrole = \"ctb\"),\nperson(given = \"Carolyn\",\nfamily = \"de Graaf\",\nrole = \"ctb\"),\nperson(given = \"Goknur\",\nfamily = \"Giner\",\nrole = \"ctb\"),\nperson(given = \"Alicia\",\nfamily = \"Oshlack\",\nrole = \"ctb\"),\nperson(given = \"Marcus\",\nfamily = \"Davy\",\nrole = \"ctb\"),\nperson(given = \"Mette\",\nfamily = \"Langaas\",\nrole = \"ctb\"),\nperson(given = \"Egil\",\nfamily = \"Ferkingstad\",\nrole = \"ctb\"),\nperson(given = \"Francois\",\nfamily = \"Pepin\",\nrole = \"ctb\"),\nperson(given = \"Dongseok\",\nfamily = \"Choi\",\nrole = \"ctb\")\n)", "License": "GPL (>=2)", "VignetteBuilder": "knitr", "URL": "https://bioinf.wehi.edu.au/limma/", "biocViews": "ExonArray, GeneExpression, Transcription,\nAlternativeSplicing, DifferentialExpression,\nDifferentialSplicing, GeneSetEnrichment, DataImport, Bayesian,\nClustering, Regression, TimeCourse, Microarray, MicroRNAArray,\nmRNAMicroarray, OneChannel, ProprietaryPlatforms, TwoChannel,\nSequencing, RNASeq, BatchEffect, MultipleComparison,\nNormalization, Preprocessing, QualityControl,\nBiomedicalInformatics, CellBiology, Cheminformatics,\nEpigenetics, FunctionalGenomics, Genetics, ImmunoOncology,\nMetabolomics, Proteomics, SystemsBiology, Transcriptomics", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-11-01 07:12:50 UTC", "RemoteUrl": "https://github.com/bioc/limma", "RemoteRef": "HEAD", "RemoteSha": "498f86398f0cb3ad2f74fa3d3588155c0d1f51c9", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-01 20:46:30 UTC", "User": "root" }, "Author": "Gordon Smyth [cre, aut] (ORCID:\n),\nLizhong Chen [aut] (ORCID: ),\nMatthew Ritchie [ctb],\nBelinda Phipson [ctb],\nDi Wu [ctb],\nYifang Hu [ctb],\nCharity Law [ctb],\nWei Shi [ctb],\nJames Wettenhall [ctb],\nYunshun Chen [ctb],\nMengbo Li [ctb],\nJeremy Silver [ctb],\nAaron Lun [ctb],\nDavis McCarthy [ctb],\nNatalie Thorne [ctb],\nCarolyn de Graaf [ctb],\nGoknur Giner [ctb],\nAlicia Oshlack [ctb],\nMarcus Davy [ctb],\nMette Langaas [ctb],\nEgil Ferkingstad [ctb],\nFrancois Pepin [ctb],\nDongseok Choi [ctb]", "Maintainer": "Gordon Smyth ", "_user": "bioc", "_type": "src", "_file": "limma_3.99.4.tar.gz", "_fileid": "https://r2.ropensci.org/317c488fa9811778f68618f144536170045f42de38b0fb9a269d5a3fd7f7b602", "_filesize": 3741527, "_sha256": "317c488fa9811778f68618f144536170045f42de38b0fb9a269d5a3fd7f7b602", "_expires": "2027-02-09T23:49:21.000Z", "_created": "2026-11-01T20:46:30.000Z", "_published": "2026-11-01T23:49:23.766Z", "_upstream": "https://github.com/bioc/limma", "_status": "success", "_maintainer": { 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"topics": [ "07.SingleChannel" ] }, { "page": "08Tests", "title": "Topic: Hypothesis Testing for Linear Models", "topics": [ "08.Tests" ] }, { "page": "09Diagnostics", "title": "Topic: Diagnostics and Quality Assessment", "topics": [ "09.Diagnostics" ] }, { "page": "10GeneSetTests", "title": "Topic: Gene Set Tests", "concept": [ "gene set tests" ], "topics": [ "10.GeneSetTests" ] }, { "page": "11RNAseq", "title": "Topic: Analysis of RNA-seq Data", "topics": [ "11.RNAseq" ] }, { "page": "alias2Symbol", "title": "Convert Gene Aliases to Official Gene Symbols", "topics": [ "alias2Symbol", "alias2SymbolTable", "alias2SymbolUsingNCBI" ] }, { "page": "anova-method", "title": "ANOVA Table - method", "topics": [ "anova.MAList" ] }, { "page": "arrayWeights", "title": "Array Quality Weights", "topics": [ "arrayWeights" ] }, { "page": "arrayWeightsQuick", "title": "Array Quality Weights", "topics": [ "arrayWeightsQuick" ] }, { "page": "asdataframe", "title": "Turn a Microarray Linear Model Object into a Dataframe", "topics": [ "as.data.frame.EList", "as.data.frame.EListRaw", "as.data.frame.MAList", "as.data.frame.MArrayLM" ] }, { "page": "asmalist", "title": "Convert marrayNorm Object to an MAList Object", "topics": [ "as.MAList" ] }, { "page": "asmatrix", "title": "Turn a Microarray Data Object into a Matrix", "topics": [ "as.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" ] }, { "page": "asMatrixWeights", "title": "asMatrixWeights", "topics": [ "asMatrixWeights" ] }, { "page": "auROC", "title": "Area Under Receiver Operating Curve", "topics": [ "auROC" ] }, { "page": "avearrays", "title": "Average Over Replicate Arrays", "topics": [ "avearrays", "avearrays.default", "avearrays.EList", "avearrays.MAList" ] }, { "page": "avedups", "title": "Average Over Duplicate Spots", "topics": [ "avedups", "avedups.default", "avedups.EList", "avedups.MAList" ] }, { "page": "avereps", "title": "Average Over Irregular Replicate Probes", "topics": [ "avereps", "avereps.default", "avereps.EList", "avereps.EListRaw", "avereps.MAList", "avereps.RGList" ] }, { "page": "backgroundcorrect", "title": "Correct Intensities for Background", "concept": [ "background correction" ], "topics": [ "backgroundCorrect", "backgroundCorrect.matrix" ] }, { "page": "barcodeplot", "title": "Barcode Enrichment Plot", "topics": [ "barcodeplot" ] }, { "page": "beadCountWeights", "title": "Bead Count Weights for Illumina BeadChips", "topics": [ "beadCountWeights" ] }, { "page": "blockDiag", "title": "Block Diagonal Matrix", "topics": [ "blockDiag" ] }, { "page": "bwss", "title": "Between and within sums of squares", "topics": [ "bwss" ] }, { "page": "bwss.matrix", "title": "Between and within sums of squares for matrix", "topics": [ "bwss.matrix" ] }, { "page": "camera", "title": "Competitive Gene Set Test Accounting for Inter-gene Correlation", "concept": [ "gene set tests" ], "topics": [ "camera", "camera.default", "cameraPR", "cameraPR.default", "interGeneCorrelation" ] }, { "page": "cbind", "title": "Combine RGList, MAList, EList or EListRaw Objects", "topics": [ "cbind", "cbind.EList", "cbind.EListRaw", "cbind.MAList", "cbind.RGList", "rbind.EList", "rbind.EListRaw", "rbind.MAList", "rbind.RGList" ] }, { "page": "changelog", "title": "Change Log", "topics": [ "changeLog" ] }, { "page": "chooseLowessSpan", "title": "Choose Span for Local-Weighted Regression Smoothing", "concept": [ "locally-weighted regression smoothing" ], "topics": [ "chooseLowessSpan" ] }, { "page": "classifytestsF", "title": "Genewise Nested F-Tests", "topics": [ "classifyTestsF" ] }, { "page": "contrastAsCoef", "title": "Reform a Design Matrix so that Contrasts Become Coefficients", "topics": [ "contrastAsCoef" ] }, { "page": "contrasts.fit", "title": "Compute Contrasts from Linear Model Fit", "topics": [ "contrasts.fit" ] }, { "page": "controlStatus", "title": "Set Status of each Spot from List of Spot Types", "topics": [ "controlStatus" ] }, { "page": "coolmap", "title": "Heatmap of gene expression values", "topics": [ "coolmap" ] }, { "page": "cumOverlap", "title": "Cumulative Overlap Analysis of Ordered Lists", "concept": [ "gene set enrichment analysis" ], "topics": [ "cumOverlap" ] }, { "page": "decideTests", "title": "Multiple Testing Across Genes and Contrasts", "topics": [ "decideTests", "decideTests.default", "decideTests.MArrayLM" ] }, { "page": "channel2M", "title": "Convert Individual Channel Design Matrix to M-A Format", "concept": [ "separate channel analysis" ], "topics": [ "designI2A", "designI2M" ] }, { "page": "detectionPValue", "title": "Detection P-Values from Negative Controls", "topics": [ "detectionPValues", "detectionPValues.default", "detectionPValues.EListRaw" ] }, { "page": "diffSplice", "title": "Differential Transcript or Exon Usage", "concept": [ "RNA-seq", "Differential transcript usage", "Differential usage" ], "topics": [ "diffSplice", "diffSplice.MArrayLM" ] }, { "page": "dim", "title": "Retrieve the Dimensions of an RGList, MAList or MArrayLM Object", "topics": [ "dim.EList", "dim.EListRaw", "dim.MAList", "dim.MArrayLM", "dim.RGList" ] }, { "page": "dimnames", "title": "Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object", "topics": [ "dimnames.EList", "dimnames.EListRaw", "dimnames.MAList", "dimnames.MArrayLM", "dimnames.RGList", "dimnames<-.EList", "dimnames<-.EListRaw", "dimnames<-.MAList", "dimnames<-.RGList" ] }, { "page": "dupcor", "title": "Correlation Between Duplicates or Within Blocks", "topics": [ "duplicateCorrelation" ] }, { "page": "ebayes", "title": "Empirical Bayes Statistics for Differential Expression", "topics": [ "eBayes", "treat" ] }, { "page": "EList", "title": "Expression List (EList) class", "topics": [ "EList-class", "EListRaw-class" ] }, { "page": "exprsMA", "title": "Extract Log-Expression Matrix from MAList", "topics": [ "exprs.MA" ] }, { "page": "fitfdist", "title": "Moment Estimation of Scaled F-Distribution", "concept": [ "empirical Bayes" ], "topics": [ "fitFDist", "fitFDistRobustly", "fitFDistUnequalDF1" ] }, { "page": "fitGammaIntercept", "title": "Fit Intercept to Vector of Gamma Distributed Variates", "topics": [ "fitGammaIntercept" ] }, { "page": "fitmixture", "title": "Fit Mixture Model by Non-Linear Least Squares", "topics": [ "fitmixture" ] }, { "page": "fitted.MArrayLM", "title": "Fitted Values Method for MArrayLM Fits", "concept": [ "regression" ], "topics": [ "fitted.MArrayLM" ] }, { "page": "genas", "title": "Genuine Association of Gene Expression Profiles", "topics": [ "genas" ] }, { "page": "geneSetTest", "title": "Mean-rank Gene Set Test", "concept": [ "gene set tests" ], "topics": [ "geneSetTest", "wilcoxGST" ] }, { "page": "getEAWP", "title": "Extract Basic Data from Expression Data Objects", "topics": [ "getEAWP" ] }, { "page": "getlayout", "title": "Extract the Print Layout of an Array from the GAL File", "topics": [ "getDupSpacing", "getLayout", "getLayout2" ] }, { "page": "getSpacing", "title": "Get Numerical Spacing", "topics": [ "getSpacing" ] }, { "page": "gls.series", "title": "Fit Linear Model to Microarray Data by Generalized Least Squares", "topics": [ "gls.series" ] }, { "page": "goana", "title": "Gene Ontology or KEGG Pathway Analysis", "concept": [ "gene set tests" ], "topics": [ "getGeneKEGGLinks", "getKEGGPathwayNames", "goana", "goana.default", "goana.MArrayLM", "kegga", "kegga.default", "kegga.MArrayLM" ] }, { "page": "goanaTrend", "title": "Estimate DE Trend for Gene Ontology or KEGG Pathway Analysis", "concept": [ "gene set tests" ], "topics": [ "goanaTrend" ] }, { "page": "gridspotrc", "title": "Row and Column Positions on Microarray", "topics": [ "gridc", "gridr", "spotc", "spotr" ] }, { "page": "head", "title": "Return the First to Last Part of a Data Object", "topics": [ "head.EList", "head.EListRaw", "head.MAList", "head.MArrayLM", "head.RGList", "head.TestResults", "tail.EList", "tail.EListRaw", "tail.MAList", "tail.MArrayLM", "tail.RGList", "tail.TestResults" ] }, { "page": "heatdiagram", "title": "Stemmed Heat Diagram", "concept": [ "plots" ], "topics": [ "heatDiagram", "heatdiagram" ] }, { "page": "helpMethods", "title": "Prompt for Method Help Topics", "topics": [ "helpMethods" ] }, { "page": "ids2indices", "title": "Convert Gene Identifiers to Indices for Gene Sets", "concept": [ "gene set tests" ], "topics": [ "ids2indices" ] }, { "page": "imageplot", "title": "Image Plot of Microarray Statistics", "topics": [ "imageplot" ] }, { "page": "imageplot3by2", "title": "Write Imageplots to Files", "topics": [ "imageplot3by2" ] }, { "page": "intraspotCorrelation", "title": "Intra-Spot Correlation for Two Color Data", "topics": [ "intraspotCorrelation" ] }, { "page": "isfullrank", "title": "Check for Full Column Rank", "topics": [ "is.fullrank", "nonEstimable" ] }, { "page": "isnumeric", "title": "Test for Numeric Argument", "topics": [ "isNumeric" ] }, { "page": "kooperberg", "title": "Kooperberg Model-Based Background Correction for GenePix data", "topics": [ "kooperberg" ] }, { "page": "LargeDataObject", "title": "Large Data Object - class", "topics": [ "LargeDataObject-class", "show,LargeDataObject-method" ] }, { "page": "limmaUsersGuide", "title": "View Limma User's Guide", "topics": [ "limmaUsersGuide" ] }, { "page": "lm.series", "title": "Fit Linear Model to Microarray Data by Ordinary Least Squares", "topics": [ "lm.series" ] }, { "page": "lmFit", "title": "Linear Model for Series of Arrays", "topics": [ "lmFit" ] }, { "page": "lmscFit", "title": "Fit Linear Model to Individual Channels of Two-Color Data", "concept": [ "separate channel analysis" ], "topics": [ "lmscFit" ] }, { "page": "loessfit", "title": "Univariate Lowess With Prior Weights", "concept": [ "locally-weighted regression smoothing" ], "topics": [ "loessFit" ] }, { "page": "logcosh", "title": "Logarithm of cosh", "concept": [ "mathematical functions" ], "topics": [ "logcosh" ] }, { "page": "logsumexp", "title": "Log Sum of Exponentials", "topics": [ "logsumexp" ] }, { "page": "ma3x3", "title": "Two dimensional Moving Averages with 3x3 Window", "topics": [ "ma3x3.matrix", "ma3x3.spottedarray" ] }, { "page": "makeContrasts", "title": "Construct Matrix of Custom Contrasts", "topics": [ "makeContrasts" ] }, { "page": "makeunique", "title": "Make Values of Character Vector Unique", "topics": [ "makeUnique" ] }, { "page": "malist", "title": "M-value, A-value Expression List - class", "topics": [ "MAList-class" ] }, { "page": "marraylm", "title": "Microarray Linear Model Fit - class", "topics": [ "MArrayLM-class" ] }, { "page": "mdplot", "title": "Mean-Difference Plot", "concept": [ "plots" ], "topics": [ "mdplot" ] }, { "page": "merge", "title": "Merge RGList or MAList Data Objects", "topics": [ "merge.EList", "merge.EListRaw", "merge.MAList", "merge.RGList" ] }, { "page": "mergeScansRG", "title": "Merge two scans of two-color arrays", "topics": [ "mergeScans", "mergeScansRG" ] }, { "page": "modelMatrix", "title": "Construct Design Matrix", "topics": [ "modelMatrix", "uniqueTargets" ] }, { "page": "modifyWeights", "title": "Modify Matrix of Weights By Control Status of Rows", "topics": [ "modifyWeights" ] }, { "page": "mrlm", "title": "Fit Linear Model to Microarray Data by Robust Regression", "topics": [ "mrlm" ] }, { "page": "nec", "title": "NormExp Background Correction and Normalization Using Control Probes", "concept": [ "background correction", "illumina beadchips" ], "topics": [ "nec", "neqc" ] }, { "page": "normalizebetweenarrays", "title": "Normalize Between Arrays", "concept": [ "normalization" ], "topics": [ "normalizeBetweenArrays", "normalizeBetweenSamples" ] }, { "page": "normalizeCyclicLoess", "title": "Normalize Columns of a Matrix by Cyclic Loess", "concept": [ "locally-weighted regression smoothing" ], "topics": [ "normalizeCyclicLoess" ] }, { "page": "normalizeprintorder", "title": "Print-Order Normalization", "topics": [ "normalizeForPrintorder", "normalizeForPrintorder.rg", "plotPrintorder" ] }, { "page": "normalizeMedianAbsValues", "title": "Normalize Columns of a Matrix to have the Median Absolute Value", "topics": [ "normalizeMedianAbsValues", "normalizeMedianValues" ] }, { "page": "normalizequantiles", "title": "Normalize Columns of a Matrix to have the same Quantiles", "topics": [ "normalizeQuantiles" ] }, { "page": "normalizeRobustSpline", "title": "Normalize Single Microarray Using Shrunk Robust Splines", "topics": [ "normalizeRobustSpline" ] }, { "page": "normalizeVSN", "title": "Variance Stabilizing Normalization (vsn)", "topics": [ "normalizeVSN", "normalizeVSN.default", "normalizeVSN.EListRaw", "normalizeVSN.RGList" ] }, { "page": "normalizeWithinArrays", "title": "Normalize Within Arrays", "topics": [ "MA.RG", "normalizeWithinArrays", "RG.MA" ] }, { "page": "normexpfit", "title": "Fit Normal+Exp Convolution Model to Observed Intensities", "topics": [ "normexp.fit" ] }, { "page": "normexpfitcontrol", "title": "Normexp Model Parameter Estimation Aided by Negative Controls", "topics": [ "normexp.fit.control" ] }, { "page": "normexpfitdetectionp", "title": "Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes", "topics": [ "normexp.fit.detection.p" ] }, { "page": "normexpsignal", "title": "Expected Signal Given Observed Foreground Under Normal+Exp Model", "topics": [ "normexp.signal" ] }, { "page": "plotDensities", "title": "Plot Expression Densities", "concept": [ "plots" ], "topics": [ "plotDensities", "plotDensities.default", "plotDensities.EList", "plotDensities.EListRaw", "plotDensities.MAList", "plotDensities.RGList" ] }, { "page": "plotExonJunc", "title": "Differential splicing plot with junctions", "concept": [ "differential usage" ], "topics": [ "plotExonJunc" ] }, { "page": "plotExons", "title": "Plot exons of differentially expressed gene", "concept": [ "differential usage" ], "topics": [ "plotExons" ] }, { "page": "plotFB", "title": "FB-Plot", "concept": [ "plots" ], "topics": [ "plotFB", "plotFB.default", "plotFB.EListRaw", "plotFB.RGList" ] }, { "page": "plotlines", "title": "plotlines", "concept": [ "plots" ], "topics": [ "plotlines" ] }, { "page": "plotma", "title": "MA-Plot of Expression Data", "topics": [ "plotMA", "plotMA.default", "plotMA.EList", "plotMA.EListRaw", "plotMA.MAList", "plotMA.MArrayLM", "plotMA.RGList" ] }, { "page": "plotma3by2", "title": "Write MA-Plots to Files", "topics": [ "plotMA3by2" ] }, { "page": "plotMD", "title": "Mean-Difference Plot of Expression Data", "concept": [ "plots" ], "topics": [ "plotMD", "plotMD.default", "plotMD.EList", "plotMD.EListRaw", "plotMD.MAList", "plotMD.MArrayLM", "plotMD.RGList" ] }, { "page": "plotMDS", "title": "Multidimensional Scaling Plot of Distances Between Expression Profiles", "concept": [ "plots" ], "topics": [ "MDS-class", "plotMDS", "plotMDS.default", "plotMDS.MDS", "show,MDS-method" ] }, { "page": "plotprinttiploess", "title": "MA Plots by Print-Tip Group", "topics": [ "plotPrintTipLoess" ] }, { "page": "plotRLDF", "title": "Plot of regularized linear discriminant functions for microarray data", "topics": [ "plotRLDF" ] }, { "page": "plotSA", "title": "Sigma vs A plot for microarray linear model", "concept": [ "plots" ], "topics": [ "plotSA" ] }, { "page": "plotSplice", "title": "Differential usage plot", "concept": [ "differential usage" ], "topics": [ "plotSplice" ] }, { "page": "plotWithHighlights", "title": "Scatterplot With Highlighting of Special Points", "topics": [ "plotWithHighlights" ] }, { "page": "poolvar", "title": "Pool Sample Variances with Unequal Variances", "topics": [ "poolVar" ] }, { "page": "predFCm", "title": "Predictive log fold change for microarrays", "concept": [ "empirical Bayes" ], "topics": [ "predFCm" ] }, { "page": "printHead", "title": "Print Leading Rows of Large Objects", "topics": [ "printHead" ] }, { "page": "PrintLayout", "title": "Print Layout - class", "topics": [ "PrintLayout-class" ] }, { "page": "printorder", "title": "Identify Order in which Spots were Printed", "topics": [ "printorder" ] }, { "page": "printtipWeights", "title": "Sub-array Quality Weights", "topics": [ "printtipWeights", "printtipWeightsSimple" ] }, { "page": "propexpr", "title": "Estimate Proportion of Expressed Probes", "topics": [ "propexpr" ] }, { "page": "propTrueNull", "title": "Estimate Proportion of True Null Hypotheses", "topics": [ "convest", "estimate.m0", "propTrueNull" ] }, { "page": "protectMetachar", "title": "Protect Metacharacters", "topics": [ "protectMetachar" ] }, { "page": "qqt", "title": "Student's t or Fisher's F Quantile-Quantile Plot", "topics": [ "qqf", "qqt" ] }, { "page": "qualwt", "title": "Spot Quality Weights for Spotted Microarrays", "topics": [ "QualityWeights", "wtarea", "wtflags", "wtIgnore.Filter" ] }, { "page": "rankSumTestwithCorrelation", "title": "Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation", "topics": [ "rankSumTestWithCorrelation" ] }, { "page": "read.columns", "title": "Read specified columns from a file", "topics": [ "read.columns" ] }, { "page": "read.idat", "title": "Read Illumina expression data from IDAT files", "concept": [ "illumina beadchips", "microarray data file" ], "topics": [ "read.idat" ] }, { "page": "read.ilmn", "title": "Read Illumina Expression Data", "concept": [ "reading data", "illumina beadchips", "microarray data file" ], "topics": [ "read.ilmn" ] }, { "page": "read.ilmn.targets", "title": "Read Illumina Data from a Target Dataframe", "concept": [ "illumina beadchips" ], "topics": [ "read.ilmn.targets" ] }, { "page": "read.maimages", "title": "Read RGList or EListRaw from Image Analysis Output Files", "concept": [ "microarray data file" ], "topics": [ "read.imagene", "read.maimages" ] }, { "page": "readgal", "title": "Read a GAL file", "topics": [ "readGAL" ] }, { "page": "readGPRHeader", "title": "Read Header Information from Microarray Raw Data File", "concept": [ "microarray data file" ], "topics": [ "readGenericHeader", "readGPRHeader", "readSMDHeader" ] }, { "page": "readImaGeneHeader", "title": "Read ImaGene Header Information", "topics": [ "readImaGeneHeader" ] }, { "page": "readSpotTypes", "title": "Read Spot Types File", "topics": [ "readSpotTypes" ] }, { "page": "readTargets", "title": "Read Targets File", "topics": [ "readTargets" ] }, { "page": "removeBatchEffect", "title": "Remove Batch Effect", "topics": [ "removeBatchEffect" ] }, { "page": "removeext", "title": "Remove Common Extension from File Names", "topics": [ "removeExt" ] }, { "page": "residuals.MArrayLM", "title": "Extract Residuals from MArrayLM Fit", "topics": [ "residuals.MArrayLM" ] }, { "page": "rglist", "title": "Red, Green Intensity List - class", "topics": [ "coerce,RGList,exprSet2-method", "RGList-class" ] }, { "page": "roast", "title": "Rotation Gene Set Tests", "concept": [ "gene set tests" ], "topics": [ "fry", "fry.default", "mroast", "mroast.default", "roast", "Roast-class", "roast.default", "show,Roast-method" ] }, { "page": "romer", "title": "Rotation Gene Set Enrichment Analysis", "concept": [ "gene set tests" ], "topics": [ "romer", "romer.default" ] }, { "page": "sampleInfoFromGEO", "title": "Read Sample Characteristics From GEO Series Matrix File", "topics": [ "sampleInfoFromGEO" ] }, { "page": "selectmodel", "title": "Select Appropriate Linear Model", "topics": [ "selectModel" ] }, { "page": "squeezeVar", "title": "Squeeze Sample Variances", "concept": [ "empirical Bayes" ], "topics": [ "squeezeVar" ] }, { "page": "strsplit2", "title": "Split Composite Names", "concept": [ "Reading data" ], "topics": [ "strsplit2" ] }, { "page": "subsetting", "title": "Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects", "topics": [ "subsetListOfArrays", "subsetting", "[.EList", "[.EListRaw", "[.MAList", "[.MArrayLM", "[.RGList", "[.TestResults" ] }, { "page": "summary", "title": "Summaries of Microarray Data Objects", "topics": [ "summary.EList", "summary.EListRaw", "summary.MAList", "summary.MArrayLM", "summary.RGList" ] }, { "page": "targetsA2C", "title": "Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel", "concept": [ "separate channel analysis" ], "topics": [ "array2channel", "targetsA2C" ] }, { "page": "TestResults", "title": "Matrix of Test Results - class", "topics": [ "labels.TestResults", "levels.TestResults", "show,TestResults-method", "summary.TestResults", "TestResults-class", "unique.TestResults" ] }, { "page": "tmixture", "title": "Estimate Scale Factor in Mixture of t-Distributions", "topics": [ "tmixture.matrix", "tmixture.vector" ] }, { "page": "topGO", "title": "Table of Top GO Terms or Top KEGG Pathways", "concept": [ "gene set tests" ], "topics": [ "topGO", "topKEGG" ] }, { "page": "topRomer", "title": "Top Gene Set Testing Results from Romer", "concept": [ "gene set tests" ], "topics": [ "topRomer" ] }, { "page": "topSplice", "title": "Top Table of Differential Transcript Usage", "concept": [ "differential usage" ], "topics": [ "topSplice" ] }, { "page": "toptable", "title": "Table of Top Genes from Linear Model Fit", "topics": [ "topTable", "topTreat" ] }, { "page": "tricubeMovingAverage", "title": "Moving Average Smoother With Tricube Weights", "concept": [ "locally-weighted regression smoothing" ], "topics": [ "tricubeMovingAverage" ] }, { "page": "trigammainverse", "title": "Inverse Trigamma Function", "concept": [ "mathematical functions" ], "topics": [ "trigammaInverse" ] }, { "page": "trimWhiteSpace", "title": "Trim Leading and Trailing White Space", "topics": [ "trimWhiteSpace" ] }, { "page": "uniquegenelist", "title": "Eliminate Duplicate Names from the Gene List", "topics": [ "uniquegenelist" ] }, { "page": "unwrapdups", "title": "Unwrap Duplicate Spot Values from Rows into Columns", 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