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 (EList) class 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 for Spotted Microarrays 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 Change Log chooseLowessSpan Choose Span for Local-Weighted Regression Smoothing classifyTestsF Genewise Nested F-Tests 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 or Within Blocks 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 head.RGList Return the First to Last Part of a Data Object 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 logsumexp Log Sum of Exponentials 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 plotExonJunc Differential splicing plot with junctions 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 or Fisher's F 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 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 readSampleInfoFromGEO Read Sample Characteristics From GEO Series Matrix File 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, MArrayLM or TestResults 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 Smoother with Prior Weights write.fit Write MArrayLM Object to a File wsva Weighted Surrogate Variable Analysis zscore Transform non-normal random deviates to standard normal zscoreT Transform t-statistics to standard normal