Linear Models for Microarray Data

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Documentation for package ‘limma’ version 3.50.3

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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
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
cameraPR Competitive Gene Set Test Accounting for Inter-gene Correlation
cameraPR.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 Change Log
chooseLowessSpan Choose Span for Local-Weighted Regression Smoothing
classifyTestsF Genewise Nested F-Tests
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 or Within Blocks

-- E --

eBayes Empirical Bayes Statistics for Differential Expression
EList-class Expression List (EList) class
EListRaw-class Expression List (EList) 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

-- 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 --

head.EList Return the First to Last Part of a Data Object
head.EListRaw Return the First to Last Part of a Data Object
head.MAList Return the First to Last Part of a Data Object
head.MArrayLM Return the First to Last Part of a Data Object
head.RGList Return the First to Last Part of a Data Object
head.TestResults Return the First to Last Part of a Data Object
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 --

labels.TestResults Matrix of Test Results - class
LargeDataObject-class Large Data Object - class
levels.TestResults Matrix of Test Results - class
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
logsumexp Log Sum of Exponentials

-- 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
plotExonJunc Differential splicing plot with junctions
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 or Fisher's F Quantile-Quantile Plot
qqt Student's t or Fisher's F Quantile-Quantile Plot
QualityWeights Spot Quality Weights for Spotted Microarrays

-- 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 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
readSampleInfoFromGEO Read Sample Characteristics From GEO Series Matrix File
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, MArrayLM or TestResults Objects
subsetting Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults 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 --

tail.EList Return the First to Last Part of a Data Object
tail.EListRaw Return the First to Last Part of a Data Object
tail.MAList Return the First to Last Part of a Data Object
tail.MArrayLM Return the First to Last Part of a Data Object
tail.RGList Return the First to Last Part of a Data Object
tail.TestResults Return the First to Last Part of a Data Object
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
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 Transform t-statistics to standard normal

-- U --

unique.TestResults Matrix of Test Results - class
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 Smoother with Prior Weights
wilcoxGST Mean-rank Gene Set Test
write.fit Write MArrayLM Object to a File
wsva Weighted Surrogate Variable Analysis
wtarea Spot Quality Weights for Spotted Microarrays
wtflags Spot Quality Weights for Spotted Microarrays
wtIgnore.Filter Spot Quality Weights for Spotted Microarrays

-- Z --

zscore Transform non-normal random deviates to standard normal
zscoreGamma Transform non-normal random deviates to standard normal
zscoreHyper Transform non-normal random deviates to standard normal
zscoreT Transform t-statistics to standard normal

-- 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, MArrayLM or TestResults Objects
[.EListRaw Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects
[.MAList Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects
[.MArrayLM Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects
[.RGList Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects
[.TestResults Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects