Function	Description
1.Introduction	Introduction to the LIMMA Package
2.Classes	Classes Defined by this Package
3.ReadingData	Reading Microarray Data from Files
4.Normalization	Normalization of Microarray Data
5.LinearModels	Linear Models for Microarrays
6.SingleChannel	Individual Channel Analysis of Two-Color Microarrays
7.Diagnostics	Diagnostics and Quality Assessment
8.Other	Other Functions
anova.MAList	ANOVA Table - method
as.MAList	Convert marrayNorm Object to an MAList Object
auROC	Area Under Receiver Operating Curve
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
cbind.RGList	Combine RGList or MAList Objects
changeLog	Limma Change Log
classifyTests	Treat Simultaneous T-Tests as Classification Problem
contrasts.fit	Compute Contrasts from Linear Model Fit
controlStatus	Set Status of each Spot from List of Spot Types
decideTests	Compute Matrix of Hypothesis Test Results
designI2M	Convert Individual Channel Design Matrix to M-A Format
designMatrix	Construct Design Matrix
dimnames.RGList	Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object
dim.RGList	Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dupcor.series	Correlation Between Duplicates
ebayes	Empirical Bayes Statistics for Differential Expression
exprSet2-class	Expression Set - class
fitFDist	Moment Estimation of Scaled F-Distribution
fit.normexp	Fit Normal+Exp Convolution Model to Observed Intensities
FStat	Treat Simultaneous T-Tests as Classification Problem
geneSetTest	Gene Set Test
getLayout	Extract the Print Layout of an Array from the GAL File
getSpacing	Get Numerical Spacing
gls.series	Generalized Least Squares for Series of Microarrays
gridr	Row and Column Positions on Microarray
heatdiagram	Stemmed Heat Diagram
helpMethods	Prompt for Method Help Topics
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
kooperberg	Kooperberg Model-Based Background Correction
LargeDataObject-class	Large Data Object - class
limmaUsersGuide	View Limma User's Guide
lmFit	Linear Model for Series of Arrays
lmscFit	Fit Linear Model to Individual Channels of Two-Color Data
lm.series	Linear Model for Series of Arrays
loessFit	Fast Simple Loess
m2loglik.normexp	Normal + Exponential Log-Likelihood
ma3x3.matrix	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
merge.RGList	Merge RGList or MAList Data Objects
modelMatrix	Construct Design Matrix
modifyWeights	modifyWeights
m.spot	Extract M or A-values from SPOT data.frame or matrix
normalizeBetweenArrays	Normalize Between Arrays
normalizeForPrintorder	Print-Order Normalization
normalizeMedianDeviations	Normalize Columns of a Matrix to have the Same Scale
normalizeQuantiles	Normalize Columns of a Matrix to have the same Quantiles
normalizeRobustSpline	Normalize Single Microarray Using Shrunk Robust Splines
normalizeWithinArrays	Normalize Within Arrays
plotDensities	Single-channel Densities Plot
plotMA	MA-Plot
plotMA3by2	Write MA-Plots to Files
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
qqt	Student's t Quantile-Quantile Plot
QualityWeights	Spot Quality Weights
readGAL	Read a GAL file
readGPRHeader	Read Header Information from Image Analysis Raw Data File
readImaGeneHeader	Read ImaGene Header Information
read.maimages	Read RGList from Image Analysis Output Files
read.matrix	Read Matrix with Headers from File
read.series	Read series of image files
readSpotTypes	Read Spot Types File
readTargets	Read RNA Targets File
removeExt	Remove Common Extension from File Names
rg.genepix	Extract RGList from data.frames Containing GenePix Data
[.RGList	Subset RGList, MAList or MArrayLM Objects
RGList-class	Red, Green Intensity List - class
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
rlm.series	Robust Linear Model for Series of Microarrays
signal.normexp	Expected Signal Given Observed Foreground Under Normal+Exp Model
splitName	Split Composite Gene Names
squeezeVar	Smooth Sample Variances
summary.RGList	Summaries of Microarray Data Objects
targetsA2C	Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
TestResults-class	Matrix of Test Results - class
tmixture.vector	Estimate Scale Factor in Mixture of t-Distributions
toptable	Table of Top Genes from Linear Model Fit
trigammaInverse	Inverse Trigamma Function
trimWhiteSpace	Trim Leading and Trailing White Space
uniquegenelist	Eliminate Duplicate Names from the Gene List
unwrapdups	Unwrap Duplicate Spot Values from Rows into Columns
vennCounts	Venn Diagrams
volcanoplot	Volcano Plot
write.fit	Write MArrayLM Object to a File
zscoreGamma	z-score equivalents