Man pages for limma
Linear Models for Microarray Data

01IntroductionIntroduction to the LIMMA Package
02classesTopic: Classes Defined by this Package
03readingTopic: Reading Microarray Data from Files
04BackgroundTopic: Background Correction
05NormalizationTopic: Normalization of Microarray Data
06linearmodelsTopic: Linear Models for Microarrays
07SingleChannelTopic: Individual Channel Analysis of Two-Color Microarrays
08TestsTopic: Hypothesis Testing for Linear Models
09DiagnosticsTopic: Diagnostics and Quality Assessment
10GeneSetTestsTopic: Gene Set Tests
11RNAseqTopic: Analysis of RNA-seq Data
alias2SymbolConvert Gene Aliases to Official Gene Symbols
anova-methodANOVA Table - method
arrayWeightsArray Quality Weights
arrayWeightsQuickArray Quality Weights
asdataframeTurn a Microarray Linear Model Object into a Dataframe
asmalistConvert marrayNorm Object to an MAList Object
asmatrixTurn a Microarray Data Object into a Matrix
asMatrixWeightsasMatrixWeights
auROCArea Under Receiver Operating Curve
avearraysAverage Over Replicate Arrays
avedupsAverage Over Duplicate Spots
averepsAverage Over Irregular Replicate Probes
backgroundcorrectCorrect Intensities for Background
barcodeplotBarcode Enrichment Plot
beadCountWeightsBead Count Weights for Illumina BeadChips
blockDiagBlock Diagonal Matrix
bwssBetween and within sums of squares
bwss.matrixBetween and within sums of squares for matrix
cameraCompetitive Gene Set Test Accounting for Inter-gene...
cbindCombine RGList, MAList, EList or EListRaw Objects
changelogLimma Change Log
channel2MConvert Individual Channel Design Matrix to M-A Format
classifytestsMultiple Testing Genewise Across Contrasts
contrastAsCoefReform a Design Matrix to that Contrasts Become Coefficients
contrasts.fitCompute Contrasts from Linear Model Fit
controlStatusSet Status of each Spot from List of Spot Types
coolmapHeatmap of gene expression values
cumOverlapCumulative Overlap Analysis of Ordered Lists
decideTestsMultiple Testing Across Genes and Contrasts
detectionPValueDetection P-Values from Negative Controls
diffSpliceTest for Differential Splicing
dimRetrieve the Dimensions of an RGList, MAList or MArrayLM...
dimnamesRetrieve the Dimension Names of an RGList, MAList, EList,...
dupcorCorrelation Between Duplicates
ebayesEmpirical Bayes Statistics for Differential Expression
ebayes-deprecatedEmpirical Bayes Statistics for Differential Expression...
EListExpression List - class
exprsMAExtract Log-Expression Matrix from MAList
fitfdistMoment Estimation of Scaled F-Distribution
fitGammaInterceptFit Intercept to Vector of Gamma Distributed Variates
fitmixtureFit Mixture Model by Non-Linear Least Squares
fitted.MArrayLMFitted Values Method for MArrayLM Fits
genasGenuine Association of Gene Expression Profiles
geneSetTestMean-rank Gene Set Test
getEAWPExtract Basic Data from Expression Data Objects
getlayoutExtract the Print Layout of an Array from the GAL File
getSpacingGet Numerical Spacing
gls.seriesFit Linear Model to Microarray Data by Generalized Least...
goanaGene Ontology or KEGG Pathway Analysis
gridspotrcRow and Column Positions on Microarray
heatdiagramStemmed Heat Diagram
helpMethodsPrompt for Method Help Topics
ids2indicesConvert Gene Identifiers to Indices for Gene Sets
imageplotImage Plot of Microarray Statistics
imageplot3by2Write Imageplots to Files
intraspotCorrelationIntra-Spot Correlation for Two Color Data
isfullrankCheck for Full Column Rank
isnumericTest for Numeric Argument
kooperbergKooperberg Model-Based Background Correction for GenePix data
LargeDataObjectLarge Data Object - class
limmaUsersGuideView Limma User's Guide
lmFitLinear Model for Series of Arrays
lmscFitFit Linear Model to Individual Channels of Two-Color Data
lm.seriesFit Linear Model to Microrray Data by Ordinary Least Squares
loessfitUnivariate Lowess With Prior Weights
logcoshLogarithm of cosh
logsumexpLog Sum of Exponentials
ma3x3Two dimensional Moving Averages with 3x3 Window
makeContrastsConstruct Matrix of Custom Contrasts
makeuniqueMake Values of Character Vector Unique
malistM-value, A-value Expression List - class
marraylmMicroarray Linear Model Fit - class
mdplotMean-Difference Plot
mergeMerge RGList or MAList Data Objects
mergeScansRGMerge two scans of two-color arrays
modelMatrixConstruct Design Matrix
modifyWeightsModify Matrix of Weights By Control Status of Rows
mrlmFit Linear Model to Microrray Data by Robust Regression
necNormExp Background Correction and Normalization Using Control...
normalizebetweenarraysNormalize Between Arrays
normalizeCyclicLoessNormalize Columns of a Matrix by Cyclic Loess
normalizeMedianAbsValuesNormalize Columns of a Matrix to have the Median Absolute...
normalizeprintorderPrint-Order Normalization
normalizequantilesNormalize Columns of a Matrix to have the same Quantiles
normalizeRobustSplineNormalize Single Microarray Using Shrunk Robust Splines
normalizeVSNVariance Stabilizing Normalization (vsn)
normalizeWithinArraysNormalize Within Arrays
normexpfitFit Normal+Exp Convolution Model to Observed Intensities
normexpfitcontrolNormexp Model Parameter Estimation Aided by Negative Controls
normexpfitdetectionpEstimate Normexp Model Parameter Using Negative Controls...
normexpsignalExpected Signal Given Observed Foreground Under Normal+Exp...
plotDensitiesPlot Expression Densities
plotExonsPlot exons of differentially expressed gene
plotFBFB-Plot
plotlinesplotlines
plotmaMA-Plot of Expression Data
plotma3by2Write MA-Plots to Files
plotMDMean-Difference Plot of Expression Data
plotMDSMultidimensional scaling plot of distances between gene...
plotprinttiploessMA Plots by Print-Tip Group
plotRLDFPlot of regularized linear discriminant functions for...
plotSASigma vs A plot for microarray linear model
plotSpliceDifferential splicing plot
plotWithHighlightsScatterplot With Highlighting of Special Points
poolvarPool Sample Variances with Unequal Variances
predFCmPredictive log fold change for microarrays
printHeadPrint Leading Rows of Large Objects
PrintLayoutPrint Layout - class
printorderIdentify Order in which Spots were Printed
printtipWeightsSub-array Quality Weights
propexprEstimate Proportion of Expressed Probes
propTrueNullEstimate Proportion of True Null Hypotheses
protectMetacharProtect Metacharacters
qqtStudent's t Quantile-Quantile Plot
qualwtSpot Quality Weights
rankSumTestwithCorrelationTwo Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For...
read.columnsRead specified columns from a file
readgalRead a GAL file
readGPRHeaderRead Header Information from Microarray Raw Data File
read.idatRead Illumina expression data directly from IDAT files
read.ilmnRead Illumina Expression Data
read.ilmn.targetsRead Illumina Data from a Target Dataframe
readImaGeneHeaderRead ImaGene Header Information
read.maimagesRead RGList or EListRaw from Image Analysis Output Files
readSpotTypesRead Spot Types File
readTargetsRead Targets File
removeBatchEffectRemove Batch Effect
removeextRemove Common Extension from File Names
residuals.MArrayLMExtract Residuals from MArrayLM Fit
rglistRed, Green Intensity List - class
roastRotation Gene Set Tests
romerRotation Gene Set Enrichment Analysis
selectmodelSelect Appropriate Linear Model
squeezeVarSqueeze Sample Variances
strsplit2Split Composite Names
subsettingSubset RGList, MAList, EListRaw, EList or MArrayLM Objects
summarySummaries of Microarray Data Objects
targetsA2CConvert Two-Color Targets Dataframe from One-Row-Per-Array to...
TestResultsMatrix of Test Results - class
tmixtureEstimate Scale Factor in Mixture of t-Distributions
topGOTable of Top GO Terms or Top KEGG Pathways
topRomerTop Gene Set Testing Results from Romer
topSpliceTop table of differentially spliced genes or exons
toptableTable of Top Genes from Linear Model Fit
tricubeMovingAverageMoving Average Smoother With Tricube Weights
trigammainverseInverse Trigamma Function
trimWhiteSpaceTrim Leading and Trailing White Space
uniquegenelistEliminate Duplicate Names from the Gene List
unwrapdupsUnwrap Duplicate Spot Values from Rows into Columns
vennVenn Diagrams
volcanoplotVolcano Plot
voomTransform RNA-Seq Data Ready for Linear Modelling
voomaConvert Mean-Variance Trend to Observation-specific Precision...
voomWithQualityWeightsCombining observational-level with sample-specific quality...
weightedLowessLowess fit with weighting
weightedmedianWeighted Median
writefitWrite MArrayLM Object to a File
wsvaWeighted Surrogate Variable Analysis
zscoreZ-score Equivalents
limma documentation built on June 22, 2018, 6 p.m.