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.Diagnostics           Diagnostics and Quality Assessment
LargeDataObject-class   Large Data Object - class
PrintLayout             Print Layout - class
anova.MAList-method     ANOVA Table - method
as.MAList               Convert marrayNorm Object to an MAList Object
backgroundCorrect       Correct Intensities for Background
bwss                    Between and within sums of squares
bwss.matrix             Between and within sums of squares for matrix
cbind                   Combine RGList or MAList Objects
classifyTests           Treat Simultaneous T-Tests as Classification
                        Problem
contrasts.fit           Contrast Information from Linear Model Fit
controlStatus           Get Spot Status from Spot Types
designMatrix            Construct Design Matrix
dim                     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
getLayout               Extract the Print Layout of an Array from the
                        GAL File
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
is.fullrank             Check for Full Column Rank
isNumeric               Test for Numeric Argument
kooperberg              Kooperberg Model-Based Background Correction
lm.series               Linear Model for Series of Arrays
lmFit                   Linear Model for Series of Arrays
loessFit                Fast Simple Loess
m.spot                  Extract M or A-values from SPOT data.frame or
                        matrix
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 Data Objects
normalizeRobustSpline   Normalize Single Microarray Using Shrunk
                        Robust Splines
normalizeWithinArrays   Normalize Within Arrays
normalizeBetweenArrays
                        Normalize Between Arrays
normalizeForPrintorder
                        Print-Order Normalization
normalizeQuantiles      Normalize Columns of a Matrix to have the same
                        Quantiles
normalizeScale          Normalize Columns of a Matrix to have the Same
                        Scale
plotDensities           Single-channel Densities Plot
plotMA                  MA-Plot
plotPrintTipLoess       MA Plots by Print-Tip Group
printHead               Print Leading Rows of Large Objects
printorder              Identify Order in which Spots were Printed
qqt                     Student's t Quantile-Quantile Plot
QualityWeights          Spot Quality Weights
read.maimages           Read RGList from Image Analysis Output Files
read.matrix             Read Matrix with Headers from File
read.series             Read series of image files
readGPRHeaders          Read GenePix Results File Header Information
readImageneHeaders      Read Imagene Header Information
readSpotTypes           Read Spot Types File
readTargets             Read RNA Targets File
readGAL                 Read a GAL file
removeExt               Remove Common Extension from File Names
rg.genepix              Extract RGList from data.frames Containing
                        Genepix Data
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              Robust Linear Model for Series of Microarrays
splitName               Split Composite Gene Names
subsetting              Subset RGList or MAList Objects
tmixture                Estimate Scale Factor in Mixture of
                        t-Distributions
toptable                Table of Top Genes from Linear Model Fit
trigammaInverse         Inverse Trigamma Function
uniquegenelist          Eliminate Duplicate Names from the Gene List
unwrapdups              Unwrap Duplicate Spot Values from Rows into
                        Columns
venn                    Venn Diagrams
zscore                  z-score equivalents
