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 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 [.RGList Subset RGList, MAList or MArrayLM Objects 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.MArrayLM 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 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 exprs.MA Extract Log-Expression Matrix from MAList fitFDist Moment Estimation of Scaled F-Distribution fitted.MArrayLM Fitted Values Method for MArrayLM Fits 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 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 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 plotlines plotlines poolVar Pool Sample Variances with Unequal Variances printHead Print Leading Rows of Large Objects printorder Identify Order in which Spots were Printed protectMetachar Protect Metacharacters qqt Student's t Quantile-Quantile Plot 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 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 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