# Linear Models for Microarray Data

## Documentation for package `limma' version 2.8.1

## User Guides and Package Vignettes

Read overview or 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

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

## -- A --

a.spot | Extract M or A-values from SPOT data.frame or matrix
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.MArrayLM | Turn a Microarray Linear Model Object into a Dataframe
as.MAList | Convert marrayNorm Object to an MAList Object
as.matrix.exprSet | 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
asMatrixWeights | asMatrixWeights
auROC | Area Under Receiver Operating Curve
avedups | Average Over Duplicate Spots

## -- B --

backgroundCorrect | Correct Intensities for Background
blockDiag | Block Diagonal Matrix
bwss | Between and within sums of squares
bwss.matrix | Between and within sums of squares for matrix

## -- C --

cbind.MAList | Combine RGList or MAList Objects
cbind.RGList | Combine RGList or MAList Objects
changeLog | Limma Change Log
classifyTestsF | Multiple Testing Genewise Across Contrasts
classifyTestsP | Multiple Testing Genewise Across Contrasts
classifyTestsT | Multiple Testing Genewise Across Contrasts
coerce,RGList,exprSet2-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.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.MAList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object
dimnames.MArrayLM | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object
dimnames.RGList | Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object
dnormexp | The Normal + Exponential Convolution Distribution
duplicateCorrelation | Correlation Between Duplicates

## -- E --

eBayes | Empirical Bayes Statistics for Differential Expression
ebayes | Empirical Bayes Statistics for Differential Expression
exprs.MA | Extract Log-Expression Matrix from MAList
exprSet2-class | Expression Set - class

## -- F --

fitFDist | Moment Estimation of Scaled F-Distribution
fitted.MArrayLM | Fitted Values Method for MArrayLM Fits
FStat | Multiple Testing Genewise Across Contrasts

## -- G --

geneSetTest | Gene Set Test
getColClasses | Construct colClasses vector for use within read.table
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
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

## -- L --

LargeDataObject-class | Large Data Object - class
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
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 --

m.spot | Extract M or A-values from SPOT data.frame or matrix
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
matvec | Multiply a Matrix by a Vector
mdplot | mdplot
merge.MAList | Merge RGList or MAList Data Objects
merge.RGList | Merge RGList or MAList Data Objects
modelMatrix | Construct Design Matrix
modifyWeights | modifyWeights
mrlm | Fit Linear Model to Microrray Data by Robust Regression

## -- N --

nonEstimable | Check for Full Column Rank
normalizeBetweenArrays | Normalize Between Arrays
normalizeForPrintorder | Print-Order Normalization
normalizeMedianAbsValues | 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
normalizeWithinArrays | Normalize Within Arrays
normexp.fit | Fit Normal+Exp Convolution Model to Observed Intensities
normexp.grad | Normal + Exponential Log-Likelihood
normexp.m2loglik | Normal + Exponential Log-Likelihood
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
plotPrintorder | Print-Order Normalization
plotPrintTipLoess | MA Plots by Print-Tip Group
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
protectMetachar | Protect Metacharacters

## -- Q --

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

## -- R --

rbind.MAList | Combine RGList or MAList Objects
rbind.RGList | Combine RGList or MAList Objects
read.imagene | Read RGList from Image Analysis Output Files
read.maimages | Read RGList from Image Analysis Output Files
read.matrix | Read Matrix with Headers from File
read.series | Read series of image 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
removeExt | Remove Common Extension from File Names
residuals.MArrayLM | Extract Residuals from MArrayLM Fit
rg.genepix | Extract RGList from data.frames Containing GenePix Data
RG.MA | Normalize Within Arrays
rg.quantarray | Extract RGList from data.frames Containing Quantarray Data
rg.series.spot | Read RGList from SPOT Image Analysis Output Files
rg.spot | Extract RGList from data.frames Containing SPOT Data
RGList-class | Red, Green Intensity List - class
rlm.series | Fit Linear Model to Microrray Data by Robust Regression

## -- S --

show,LargeDataObject-method | Large Data Object - class
show,TestResults-method | Matrix of Test Results - class
splitName | Split Composite Gene Names
spotc | Row and Column Positions on Microarray
spotr | Row and Column Positions on Microarray
squeezeVar | Smooth Sample Variances
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
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
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 --

vecmat | Multiply a Matrix by a Vector
vennCounts | Venn Diagrams
vennDiagram | Venn Diagrams
volcanoplot | Volcano Plot

## -- W --

weighted.median | Weighted Median
write.fit | Write MArrayLM Object to a File
wtarea | Spot Quality Weights
wtflags | Spot Quality Weights
wtIgnore.Filter | Spot Quality Weights
wtVariables | Read RGList from Image Analysis Output Files

## -- Z --

zscoreGamma | Z-score Equivalents
zscoreT | Z-score Equivalents

## -- misc --

[.MAList | Subset RGList, MAList or MArrayLM Objects
[.MArrayLM | Subset RGList, MAList or MArrayLM Objects
[.RGList | Subset RGList, MAList or MArrayLM Objects