[.RGList                Subset RGList, MAList or MArrayLM Objects
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
anova.MAList            ANOVA Table - method
arrayWeights            Array Quality Weights
arrayWeightsQuick       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.RGList        Turn a Microarray Data Object into a Matrix
asMatrixWeights         asMatrixWeights
auROC                   Area Under Receiver Operating Curve
avedups                 Average Over Duplicate Spots
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
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
decideTests             Multiple Testing Across Genes and Contrasts
designI2M               Convert Individual Channel Design Matrix to M-A
                        Format
dim.RGList              Retrieve the Dimensions 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
ebayes                  Empirical Bayes Statistics for Differential
                        Expression
exprSet2-class          Expression Set - class
fitFDist                Moment Estimation of Scaled F-Distribution
fitted.MArrayLM         Fitted Values Method for MArrayLM Fits
FStat                   Multiple Testing Genewise Across Contrasts
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
getSpacing              Get Numerical Spacing
gls.series              Fit Linear Model to Microarray Data by
                        Generalized Least Squares
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
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.spot                  Extract M or A-values from SPOT data.frame or
                        matrix
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
mdplot                  mdplot
merge.RGList            Merge RGList or MAList Data Objects
modelMatrix             Construct Design Matrix
modifyWeights           modifyWeights
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.m2loglik        Normal + Exponential Log-Likelihood
normexp.signal          Expected Signal Given Observed Foreground Under
                        Normal+Exp Model
plotDensities           Individual-channel Densities Plot
plotFB                  FB-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
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
readImaGeneHeader       Read ImaGene Header Information
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.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
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
weighted.median         Weighted Median
write.fit               Write MArrayLM Object to a File
wtVariables             Read RGList from Image Analysis Output Files
zscoreGamma             Z-score Equivalents
