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 avearrays Average Over Replicate Arrays avedups Average Over Duplicate Spots avereps Average Over Irregular Replicate Probes 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 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 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 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 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 Squeeze Sample Variances strsplit2 Split Composite Names subsetting Subset RGList, MAList, EList or MArrayLM Objects summary.RGList Summaries of Microarray Data Objects symbols2indices Convert Gene Set Symbols to Indices 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