Linear Models for Microarray Data

Documentation for package ‘limma’ version 3.12.0

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.

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 Alias to Official Gene Symbols
alias2SymbolTable	Convert Gene Alias 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.MAList	Average Over Irregular Replicate Probes

-- B --

backgroundCorrect	Correct Intensities for Background
backgroundCorrect.matrix	Correct Intensities for Background
barcodeplot	Barcode Plot
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
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
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

-- D --

decideTests	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
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
exprs.MA	Extract Log-Expression Matrix from MAList

-- F --

fitFDist	Moment Estimation of Scaled F-Distribution
fitted.MArrayLM	Fitted Values Method for MArrayLM Fits
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 Microarray Data Objects
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
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 --

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 --

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	Fast Simple Loess

-- 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	mdplot
MDS-class	Multidimensional scaling plot of microarray data
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	modifyWeights
mrlm	Fit Linear Model to Microrray Data by Robust Regression
mroast	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	Individual-channel Densities Plot
plotFB	FB-Plot
plotlines	plotlines
plotMA	MA-Plot
plotMA3by2	Write MA-Plots to Files
plotMDS	Multidimensional scaling plot of microarray data
plotMDS.default	Multidimensional scaling plot of microarray data
plotMDS.MDS	Multidimensional scaling plot of microarray data
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
poolVar	Pool Sample Variances with Unequal Variances
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
protectMetachar	Protect Metacharacters

-- Q --

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.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 Image Analysis Raw Data File
readGPRHeader	Read Header Information from Image Analysis Raw Data File
readImaGeneHeader	Read ImaGene Header Information
readSMDHeader	Read Header Information from Image Analysis 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
romer	Rotation Gene Set Enrichment Analysis
romer2	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 microarray data
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
subsetting	Subset RGList, MAList, 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
symbols2indices	Convert Gene Set Symbols to Indices

-- 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
topRomer	Top Gene Set Testing Results from Romer
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
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

-- W --

weighted.median	Weighted Median
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 --

zscoreGamma	Z-score Equivalents
zscoreT	Z-score Equivalents

-- misc --

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