01.Introduction         Introduction to the LIMMA Package
02.Classes              Topic: Classes Defined by this Package
03.ReadingData          Topic: Reading Microarray Data from Files
04.Background           Topic: Background Correction
05.Normalization        Topic: Normalization of Microarray Data
06.LinearModels         Topic: Linear Models for Microarrays
07.SingleChannel        Topic: Individual Channel Analysis of Two-Color
                        Microarrays
08.Tests                Topic: Hypothesis Testing for Linear Models
09.Diagnostics          Topic: Diagnostics and Quality Assessment
10.GeneSetTests         Topic: Gene Set Tests
11.RNAseq               Topic: Analysis of RNA-seq Data
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 Aliases 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
avearrays               Average Over Replicate Arrays
avedups                 Average Over Duplicate Spots
avereps                 Average Over Irregular Replicate Probes
backgroundCorrect       Correct Intensities for Background
barcodeplot             Barcode Enrichment Plot
beadCountWeights        Bead Count Weights for Illumina BeadChips
blockDiag               Block Diagonal Matrix
bwss                    Between and within sums of squares
bwss.matrix             Between and within sums of squares for matrix
camera                  Competitive Gene Set Test Accounting for
                        Inter-gene Correlation
cbind                   Combine RGList, MAList, EList or EListRaw
                        Objects
changeLog               Limma Change Log
contrastAsCoef          Reform a Design Matrix to that Contrasts Become
                        Coefficients
contrasts.fit           Compute Contrasts from Linear Model Fit
controlStatus           Set Status of each Spot from List of Spot Types
coolmap                 Heatmap of gene expression values
cumOverlap              Cumulative Overlap Analysis of Ordered Lists
decideTests             Multiple Testing Across Genes and Contrasts
designI2M               Convert Individual Channel Design Matrix to M-A
                        Format
detectionPValues        Detection P-Values from Negative Controls
diffSplice              Test for Differential Splicing
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
fitGammaIntercept       Fit Intercept to Vector of Gamma Distributed
                        Variates
fitmixture              Fit Mixture Model by Non-Linear Least Squares
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 Expression 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
goana                   Gene Ontology or KEGG Pathway Analysis
gridr                   Row and Column Positions on Microarray
heatdiagram             Stemmed Heat Diagram
helpMethods             Prompt for Method Help Topics
ids2indices             Convert Gene Identifiers to Indices for Gene
                        Sets
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
                        for GenePix data
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                Univariate Lowess With Prior Weights
logcosh                 Logarithm of cosh
ma3x3.matrix            Two dimensional Moving Averages with 3x3 Window
makeContrasts           Construct Matrix of Custom Contrasts
makeUnique              Make Values of Character Vector Unique
mdplot                  Mean-Difference Plot
merge.RGList            Merge RGList or MAList Data Objects
mergeScans              Merge two scans of two-color arrays
modelMatrix             Construct Design Matrix
modifyWeights           Modify Matrix of Weights By Control Status of
                        Rows
mrlm                    Fit Linear Model to Microrray Data by Robust
                        Regression
nec                     NormExp Background Correction and Normalization
                        Using Control Probes
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
normalizeVSN            Variance Stabilizing Normalization (vsn)
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.fit.detection.p
                        Estimate Normexp Model Parameter Using Negative
                        Controls Inferred from Regular Probes
normexp.signal          Expected Signal Given Observed Foreground Under
                        Normal+Exp Model
plotDensities           Plot Expression Densities
plotExons               Plot exons of differentially expressed gene
plotFB                  FB-Plot
plotMA                  MA-Plot of Expression Data
plotMA3by2              Write MA-Plots to Files
plotMD                  Mean-Difference Plot of Expression Data
plotMDS                 Multidimensional scaling plot of distances
                        between gene expression profiles
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
plotSplice              Differential splicing plot
plotWithHighlights      Scatterplot With Highlighting of Special Points
plotlines               plotlines
poolVar                 Pool Sample Variances with Unequal Variances
predFCm                 Predictive log fold change for microarrays
printHead               Print Leading Rows of Large Objects
printorder              Identify Order in which Spots were Printed
printtipWeights         Sub-array Quality Weights
propTrueNull            Estimate Proportion of True Null Hypotheses
propexpr                Estimate Proportion of Expressed Probes
protectMetachar         Protect Metacharacters
qqt                     Student's t Quantile-Quantile Plot
rankSumTestWithCorrelation
                        Two Sample Wilcoxon-Mann-Whitney Rank Sum Test
                        Allowing For Correlation
read.columns            Read specified columns from a file
read.idat               Read Illumina expression data directly from
                        IDAT files
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 Microarray 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              Squeeze Sample Variances
strsplit2               Split Composite Names
subsetting              Subset RGList, MAList, EListRaw, EList or
                        MArrayLM Objects
summary.RGList          Summaries of Microarray Data Objects
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
topGO                   Table of Top GO Terms or Top KEGG Pathways
topRomer                Top Gene Set Testing Results from Romer
topSplice               Top table of differentially spliced genes or
                        exons
toptable                Table of Top Genes from Linear Model Fit
tricubeMovingAverage    Moving Average Smoother With Tricube Weights
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
voom                    Transform RNA-Seq Data Ready for Linear
                        Modelling
voomWithQualityWeights
                        Combining observational-level with
                        sample-specific quality weights for RNA-seq
                        analysis
vooma                   Convert Mean-Variance Trend to
                        Observation-specific Precision Weights for
                        Microarray Data
weighted.median         Weighted Median
weightedLowess          Lowess fit with weighting
write.fit               Write MArrayLM Object to a File
zscore                  Z-score Equivalents
