# Linear Models for Microarray Data

## Documentation for package ‘limma’ version 3.30.13

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N P Q R S T U V W Z misc

limma-package | Introduction to the LIMMA Package

## -- A --

alias2Symbol | Convert Gene Aliases to Official Gene Symbols
alias2SymbolTable | Convert Gene Aliases to Official Gene Symbols
alias2SymbolUsingNCBI | Convert Gene Aliases to Official Gene Symbols
anova.MAList | ANOVA Table - method
array2channel | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
arrayWeights | Array Quality Weights
arrayWeightsQuick | Array Quality Weights
arrayWeightsSimple | Array Quality Weights
as.data.frame.EList | Turn a Microarray Linear Model Object into a Dataframe
as.data.frame.EListRaw | Turn a Microarray Linear Model Object into a Dataframe
as.data.frame.MAList | Turn a Microarray Linear Model Object into a Dataframe
as.data.frame.MArrayLM | Turn a Microarray Linear Model Object into a Dataframe
as.MAList | Convert marrayNorm Object to an MAList Object
as.matrix.EList | Turn a Microarray Data Object into a Matrix
as.matrix.EListRaw | Turn a Microarray Data Object into a Matrix
as.matrix.ExpressionSet | Turn a Microarray Data Object into a Matrix
as.matrix.LumiBatch | Turn a Microarray Data Object into a Matrix
as.matrix.MAList | Turn a Microarray Data Object into a Matrix
as.matrix.MArrayLM | Turn a Microarray Data Object into a Matrix
as.matrix.marrayNorm | Turn a Microarray Data Object into a Matrix
as.matrix.PLMset | Turn a Microarray Data Object into a Matrix
as.matrix.RGList | Turn a Microarray Data Object into a Matrix
as.matrix.vsn | Turn a Microarray Data Object into a Matrix
asMatrixWeights | asMatrixWeights
auROC | Area Under Receiver Operating Curve
avearrays | Average Over Replicate Arrays
avearrays.default | Average Over Replicate Arrays
avearrays.EList | Average Over Replicate Arrays
avearrays.MAList | Average Over Replicate Arrays
avedups | Average Over Duplicate Spots
avedups.default | Average Over Duplicate Spots
avedups.EList | Average Over Duplicate Spots
avedups.MAList | Average Over Duplicate Spots
avereps | Average Over Irregular Replicate Probes
avereps.default | Average Over Irregular Replicate Probes
avereps.EList | Average Over Irregular Replicate Probes
avereps.EListRaw | Average Over Irregular Replicate Probes
avereps.MAList | Average Over Irregular Replicate Probes
avereps.RGList | Average Over Irregular Replicate Probes

## -- B --

backgroundCorrect | Correct Intensities for Background
backgroundCorrect.matrix | 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

## -- C --

camera | Competitive Gene Set Test Accounting for Inter-gene Correlation
camera.default | Competitive Gene Set Test Accounting for Inter-gene Correlation
cbind | Combine RGList, MAList, EList or EListRaw Objects
cbind.EList | Combine RGList, MAList, EList or EListRaw Objects
cbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects
cbind.MAList | Combine RGList, MAList, EList or EListRaw Objects
cbind.RGList | Combine RGList, MAList, EList or EListRaw Objects
changeLog | Limma Change Log
classifyTestsF | Multiple Testing Genewise Across Contrasts
classifyTestsP | Multiple Testing Genewise Across Contrasts
classifyTestsT | Multiple Testing Genewise Across Contrasts
coerce-method | Red, Green Intensity List - class
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
convest | Estimate Proportion of True Null Hypotheses
coolmap | Heatmap of gene expression values
cumOverlap | Cumulative Overlap Analysis of Ordered Lists

## -- D --

decideTests | Multiple Testing Across Genes and Contrasts
decideTests.default | Multiple Testing Across Genes and Contrasts
decideTests.MArrayLM | Multiple Testing Across Genes and Contrasts
designI2A | Convert Individual Channel Design Matrix to M-A Format
designI2M | Convert Individual Channel Design Matrix to M-A Format
detectionPValues | Detection P-Values from Negative Controls
detectionPValues.default | Detection P-Values from Negative Controls
detectionPValues.EListRaw | Detection P-Values from Negative Controls
diffSplice | Test for Differential Splicing
dim.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dimnames.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames<-.EList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames<-.EListRaw | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames<-.MAList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
dimnames<-.RGList | Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
duplicateCorrelation | Correlation Between Duplicates

## -- E --

eBayes | Empirical Bayes Statistics for Differential Expression
ebayes | Empirical Bayes Statistics for Differential Expression
EList-class | Expression List - class
EListRaw-class | Expression List - class
estimate.m0 | Estimate Proportion of True Null Hypotheses
exprs.MA | Extract Log-Expression Matrix from MAList

## -- F --

fitFDist | Moment Estimation of Scaled F-Distribution
fitFDistRobustly | 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
fry | Rotation Gene Set Tests
fry.default | Rotation Gene Set Tests
FStat | Multiple Testing Genewise Across Contrasts

## -- G --

genas | Genuine Association of Gene Expression Profiles
geneSetTest | Mean-rank Gene Set Test
getDupSpacing | Extract the Print Layout of an Array from the GAL File
getEAWP | Extract Basic Data from Expression Data Objects
getGeneKEGGLinks | Gene Ontology or KEGG Pathway Analysis
getKEGGPathwayNames | Gene Ontology or KEGG Pathway Analysis
getLayout | Extract the Print Layout of an Array from the GAL File
getLayout2 | 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 Squares
goana | Gene Ontology or KEGG Pathway Analysis
goana.default | Gene Ontology or KEGG Pathway Analysis
goana.MArrayLM | Gene Ontology or KEGG Pathway Analysis
gridc | Row and Column Positions on Microarray
gridr | Row and Column Positions on Microarray

## -- H --

heatDiagram | Stemmed Heat Diagram
heatdiagram | Stemmed Heat Diagram
helpMethods | Prompt for Method Help Topics

## -- I --

ids2indices | Convert Gene Identifiers to Indices for Gene Sets
imageplot | Image Plot of Microarray Statistics
imageplot3by2 | Write Imageplots to Files
interGeneCorrelation | Competitive Gene Set Test Accounting for Inter-gene Correlation
intraspotCorrelation | Intra-Spot Correlation for Two Color Data
is.fullrank | Check for Full Column Rank
isNumeric | Test for Numeric Argument

## -- K --

kegga | Gene Ontology or KEGG Pathway Analysis
kegga.default | Gene Ontology or KEGG Pathway Analysis
kegga.MArrayLM | Gene Ontology or KEGG Pathway Analysis
kooperberg | Kooperberg Model-Based Background Correction for GenePix data

## -- L --

LargeDataObject-class | Large Data Object - class
length.EList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.EListRaw | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.MAList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.MArrayLM | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.RGList | Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
limma | Introduction to the LIMMA Package
limmaUsersGuide | View Limma User's Guide
lm.series | Fit Linear Model to Microrray Data by Ordinary Least Squares
lmFit | Linear Model for Series of Arrays
lmscFit | Fit Linear Model to Individual Channels of Two-Color Data
loessFit | Univariate Lowess With Prior Weights
logcosh | Logarithm of cosh

## -- M --

MA.RG | Normalize Within Arrays
ma3x3.matrix | Two dimensional Moving Averages with 3x3 Window
ma3x3.spottedarray | Two dimensional Moving Averages with 3x3 Window
makeContrasts | Construct Matrix of Custom Contrasts
makeUnique | Make Values of Character Vector Unique
MAList-class | M-value, A-value Expression List - class
MArrayLM-class | Microarray Linear Model Fit - class
mdplot | Mean-Difference Plot
MDS-class | Multidimensional scaling plot of distances between gene expression profiles
merge.EList | Merge RGList or MAList Data Objects
merge.EListRaw | Merge RGList or MAList Data Objects
merge.MAList | Merge RGList or MAList Data Objects
merge.RGList | Merge RGList or MAList Data Objects
mergeScans | Merge two scans of two-color arrays
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
mroast | Rotation Gene Set Tests
mroast.default | Rotation Gene Set Tests

## -- N --

nec | NormExp Background Correction and Normalization Using Control Probes
neqc | NormExp Background Correction and Normalization Using Control Probes
nonEstimable | Check for Full Column Rank
normalizeBetweenArrays | Normalize Between Arrays
normalizeCyclicLoess | Normalize Columns of a Matrix by Cyclic Loess
normalizeForPrintorder | Print-Order Normalization
normalizeForPrintorder.rg | Print-Order Normalization
normalizeMedianAbsValues | Normalize Columns of a Matrix to have the Median Absolute Value
normalizeMedianValues | Normalize Columns of a Matrix to have the Median Absolute Value
normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles
normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines
normalizeVSN | Variance Stabilizing Normalization (vsn)
normalizeVSN.default | Variance Stabilizing Normalization (vsn)
normalizeVSN.EListRaw | Variance Stabilizing Normalization (vsn)
normalizeVSN.RGList | Variance Stabilizing Normalization (vsn)
normalizeWithinArrays | Normalize Within Arrays
normexp.fit | Fit Normal+Exp Convolution Model to Observed Intensities
normexp.fit.control | Normexp Model Parameter Estimation Aided by Negative Controls
normexp.fit.detection.p | Estimate Normexp Model Parameter Using Negative Controls Inferred from Regular Probes
normexp.signal | Expected Signal Given Observed Foreground Under Normal+Exp Model

## -- P --

plotDensities | Plot Expression Densities
plotDensities.default | Plot Expression Densities
plotDensities.EList | Plot Expression Densities
plotDensities.EListRaw | Plot Expression Densities
plotDensities.MAList | Plot Expression Densities
plotDensities.RGList | Plot Expression Densities
plotExons | Plot exons of differentially expressed gene
plotFB | FB-Plot
plotFB.default | FB-Plot
plotFB.EListRaw | FB-Plot
plotFB.RGList | FB-Plot
plotlines | plotlines
plotMA | MA-Plot of Expression Data
plotMA.default | MA-Plot of Expression Data
plotMA.EList | MA-Plot of Expression Data
plotMA.EListRaw | MA-Plot of Expression Data
plotMA.MAList | MA-Plot of Expression Data
plotMA.MArrayLM | MA-Plot of Expression Data
plotMA.RGList | MA-Plot of Expression Data
plotMA3by2 | Write MA-Plots to Files
plotMD | Mean-Difference Plot of Expression Data
plotMD.default | Mean-Difference Plot of Expression Data
plotMD.EList | Mean-Difference Plot of Expression Data
plotMD.EListRaw | Mean-Difference Plot of Expression Data
plotMD.MAList | Mean-Difference Plot of Expression Data
plotMD.MArrayLM | Mean-Difference Plot of Expression Data
plotMD.RGList | Mean-Difference Plot of Expression Data
plotMDS | Multidimensional scaling plot of distances between gene expression profiles
plotMDS.default | Multidimensional scaling plot of distances between gene expression profiles
plotMDS.MDS | Multidimensional scaling plot of distances between gene expression profiles
plotPrintorder | Print-Order Normalization
plotPrintTipLoess | MA Plots by Print-Tip Group
plotRLDF | Plot of regularized linear discriminant functions for microarray data
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-class | Print Layout - class
printorder | Identify Order in which Spots were Printed
printtipWeights | Sub-array Quality Weights
printtipWeightsSimple | Sub-array Quality Weights
propexpr | Estimate Proportion of Expressed Probes
propTrueNull | Estimate Proportion of True Null Hypotheses
protectMetachar | Protect Metacharacters

## -- Q --

qqf | Student's t Quantile-Quantile Plot
qqt | Student's t Quantile-Quantile Plot
QualityWeights | Spot Quality Weights

## -- R --

rankSumTestWithCorrelation | Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation
rbind.EList | Combine RGList, MAList, EList or EListRaw Objects
rbind.EListRaw | Combine RGList, MAList, EList or EListRaw Objects
rbind.MAList | Combine RGList, MAList, EList or EListRaw Objects
rbind.RGList | Combine RGList, MAList, EList or EListRaw Objects
read.columns | Read specified columns from a 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
read.imagene | Read RGList or EListRaw from Image Analysis Output Files
read.maimages | Read RGList or EListRaw from Image Analysis Output Files
readGAL | Read a GAL file
readGenericHeader | Read Header Information from Microarray Raw Data File
readGPRHeader | Read Header Information from Microarray Raw Data File
readImaGeneHeader | Read ImaGene Header Information
readSMDHeader | Read Header Information from Microarray Raw Data File
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
RG.MA | Normalize Within Arrays
RGList-class | Red, Green Intensity List - class
roast | Rotation Gene Set Tests
Roast-class | Rotation Gene Set Tests
roast.default | Rotation Gene Set Tests
romer | Rotation Gene Set Enrichment Analysis
romer.default | Rotation Gene Set Enrichment Analysis

## -- S --

selectModel | Select Appropriate Linear Model
show-method | Large Data Object - class
show-method | Matrix of Test Results - class
show-method | Multidimensional scaling plot of distances between gene expression profiles
show-method | Rotation Gene Set Tests
spotc | Row and Column Positions on Microarray
spotr | Row and Column Positions on Microarray
squeezeVar | Squeeze Sample Variances
strsplit2 | Split Composite Names
subsetListOfArrays | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
subsetting | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
summary.EList | Summaries of Microarray Data Objects
summary.EListRaw | Summaries of Microarray Data Objects
summary.MAList | Summaries of Microarray Data Objects
summary.MArrayLM | Summaries of Microarray Data Objects
summary.RGList | Summaries of Microarray Data Objects
summary.TestResults | Matrix of Test Results - class

## -- T --

targetsA2C | Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
TestResults-class | Matrix of Test Results - class
tmixture.matrix | Estimate Scale Factor in Mixture of t-Distributions
tmixture.vector | Estimate Scale Factor in Mixture of t-Distributions
topGO | Table of Top GO Terms or Top KEGG Pathways
topKEGG | 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
toptable | Table of Top Genes from Linear Model Fit
topTableF | Table of Top Genes from Linear Model Fit
topTreat | Table of Top Genes from Linear Model Fit
treat | Empirical Bayes Statistics for Differential Expression
tricubeMovingAverage | Moving Average Smoother With Tricube Weights
trigammaInverse | Inverse Trigamma Function
trimWhiteSpace | Trim Leading and Trailing White Space
tZscore | Z-score Equivalents

## -- U --

uniquegenelist | Eliminate Duplicate Names from the Gene List
uniqueTargets | Construct Design Matrix
unwrapdups | Unwrap Duplicate Spot Values from Rows into Columns

## -- V --

vennCounts | Venn Diagrams
vennDiagram | Venn Diagrams
volcanoplot | Volcano Plot
voom | Transform RNA-Seq Data Ready for Linear Modelling
vooma | Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data
voomaByGroup | Convert Mean-Variance Trend to Observation-specific Precision Weights for Microarray Data
voomWithQualityWeights | Combining observational-level with sample-specific quality weights for RNA-seq analysis

## -- W --

weighted.median | Weighted Median
weightedLowess | Lowess fit with weighting
wilcoxGST | Mean-rank Gene Set Test
write.fit | Write MArrayLM Object to a File
wtarea | Spot Quality Weights
wtflags | Spot Quality Weights
wtIgnore.Filter | Spot Quality Weights

## -- Z --

zscore | Z-score Equivalents
zscoreGamma | Z-score Equivalents
zscoreHyper | Z-score Equivalents
zscoreT | Z-score Equivalents

## -- misc --

01.Introduction | Introduction to the LIMMA Package
02.Classes | Topic: Classes Defined by this Package
03.ReadingData | Topic: Reading Microarray Data from Files
04.Background | Topic: Background Correction
05.Normalization | Topic: Normalization of Microarray Data
06.LinearModels | Topic: Linear Models for Microarrays
07.SingleChannel | Topic: Individual Channel Analysis of Two-Color Microarrays
08.Tests | Topic: Hypothesis Testing for Linear Models
09.Diagnostics | Topic: Diagnostics and Quality Assessment
10.GeneSetTests | Topic: Gene Set Tests
11.RNAseq | Topic: Analysis of RNA-seq Data
[.EList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
[.EListRaw | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
[.MAList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
[.MArrayLM | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects
[.RGList | Subset RGList, MAList, EListRaw, EList or MArrayLM Objects