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-class             Expression List - class
FStat                   Multiple Testing Genewise Across Contrasts
LargeDataObject-class   Large Data Object - class
MAList-class            M-value, A-value Expression List - class
MArrayLM-class          Microarray Linear Model Fit - class
PrintLayout-class       Print Layout - class
QualityWeights          Spot Quality Weights
RGList-class            Red, Green Intensity List - class
TestResults-class       Matrix of Test Results - class
alias2Symbol            Convert Gene Alias to Official Gene Symbols
anova.MAList            ANOVA Table - method
arrayWeights            Array Quality Weights
arrayWeightsQuick       Array Quality Weights
as.MAList               Convert marrayNorm Object to an MAList Object
as.data.frame.MAList    Turn a Microarray Linear Model Object into a
                        Dataframe
as.matrix.RGList        Turn a Microarray Data Object into a Matrix
asMatrixWeights         asMatrixWeights
auROC                   Area Under Receiver Operating Curve
avedups                 Average Over Duplicate Spots
avereps                 Average Over Irregular Replicate 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                   Combine RGList, MAList, EList or EListRaw
                        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, EList, EListRaw or MArrayLM Object
duplicateCorrelation    Correlation Between Duplicates
ebayes                  Empirical Bayes Statistics for Differential
                        Expression
exprs.MA                Extract Log-Expression Matrix from MAList
fitFDist                Moment Estimation of Scaled F-Distribution
fitted.MArrayLM         Fitted Values Method for MArrayLM Fits
genas                   Genuine Association of Gene Expression Profiles
geneSetTest             Mean-rank Gene Set Test
getEAWP                 Extract Basic Data from Microarray Data Objects
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
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
ma3x3.matrix            Two dimensional Moving Averages with 3x3 Window
makeContrasts           Construct Matrix of Custom Contrasts
makeUnique              Make Values of Character Vector Unique
mdplot                  mdplot
merge.RGList            Merge RGList or MAList Data Objects
mergeScans              Merge two scans of two-color arrays
modelMatrix             Construct Design Matrix
modifyWeights           modifyWeights
mrlm                    Fit Linear Model to Microrray Data by Robust
                        Regression
neqc                    NormExp and Quantile by Control (NEQC)
normalizeBetweenArrays
                        Normalize Between Arrays
normalizeCyclicLoess    Normalize Columns of a Matrix by Cyclic Loess
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.fit.control     Normexp Model Parameter Estimation Aided by
                        Negative Controls
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
plotMDS                 Multidimensional scaling plot of microarray
                        data
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
plotlines               plotlines
poolVar                 Pool Sample Variances with Unequal Variances
printHead               Print Leading Rows of Large Objects
printorder              Identify Order in which Spots were Printed
printtipWeights         Sub-array Quality Weights
propexpr                Estimate Proportion of Expressed Probes
protectMetachar         Protect Metacharacters
qqt                     Student's t Quantile-Quantile Plot
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.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
readImaGeneHeader       Read ImaGene Header Information
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
roast                   Rotation Gene Set Tests
romer                   Rotation Gene Set Enrichment Analysis
selectModel             Select Appropriate Linear Model
squeezeVar              Smooth Sample Variances
strsplit2               Split Composite Names
subsetting              Subset RGList, MAList, EList or MArrayLM
                        Objects
summary.RGList          Summaries of Microarray Data Objects
symbols2indices         Make Gene Set Indices from Symbols
targetsA2C              Convert Two-Color Targets Dataframe from
                        One-Row-Per-Array to One-Row-Per-Channel
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
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
zscoreGamma             Z-score Equivalents
