Entry: 01.Introduction
Aliases: 01.Introduction limma
Keywords: documentation
Description: Introduction to the LIMMA Package
URL: ../../../library/limma/html/01Introduction.html

Entry: 02.Classes
Aliases: 02.Classes
Keywords: documentation
Description: Classes Defined by this Package
URL: ../../../library/limma/html/02classes.html

Entry: 03.ReadingData
Aliases: 03.ReadingData
Keywords: documentation
Description: Reading Microarray Data from Files
URL: ../../../library/limma/html/03reading.html

Entry: 04.Background
Aliases: 04.Background
Keywords: documentation
Description: Background Correction
URL: ../../../library/limma/html/04Background.html

Entry: 05.Normalization
Aliases: 05.Normalization
Keywords: documentation
Description: Normalization of Microarray Data
URL: ../../../library/limma/html/05Normalization.html

Entry: 06.LinearModels
Aliases: 06.LinearModels
Keywords: documentation
Description: Linear Models for Microarrays
URL: ../../../library/limma/html/06linearmodels.html

Entry: 07.SingleChannel
Aliases: 07.SingleChannel
Keywords: documentation
Description: Individual Channel Analysis of Two-Color Microarrays
URL: ../../../library/limma/html/07SingleChannel.html

Entry: 08.Tests
Aliases: 08.Tests
Keywords: documentation
Description: Hypothesis Testing for Linear Models
URL: ../../../library/limma/html/08Tests.html

Entry: 09.Diagnostics
Aliases: 09.Diagnostics
Keywords: documentation
Description: Diagnostics and Quality Assessment
URL: ../../../library/limma/html/09Diagnostics.html

Entry: 10.Other
Aliases: 10.Other
Keywords: documentation
Description: Other Functions
URL: ../../../library/limma/html/10Other.html

Entry: EList-class
Aliases: EList-class EListRaw-class
Keywords: classes data
Description: Expression List - class
URL: ../../../library/limma/html/EList.html

Entry: LargeDataObject-class
Aliases: LargeDataObject-class show,LargeDataObject-method
Keywords: classes data
Description: Large Data Object - class
URL: ../../../library/limma/html/LargeDataObject.html

Entry: PrintLayout
Aliases: PrintLayout-class
Keywords: classes data
Description: Print Layout - class
URL: ../../../library/limma/html/PrintLayout.html

Entry: TestResults-class
Aliases: TestResults-class show,TestResults-method summary.TestResults
Keywords: classes htest
Description: Matrix of Test Results - class
URL: ../../../library/limma/html/TestResults.html

Entry: alias2Symbol
Aliases: alias2Symbol
Keywords: character
Description: Convert Gene Alias to Official Gene Symbols
URL: ../../../library/limma/html/alias2Symbol.html

Entry: anova.MAList-method
Aliases: anova.MAList
Keywords: models
Description: ANOVA Table - method
URL: ../../../library/limma/html/anova-method.html

Entry: arrayWeights
Aliases: arrayWeights arrayWeightsSimple
Keywords: regression models
Description: Array Quality Weights
URL: ../../../library/limma/html/arrayWeights.html

Entry: arrayWeightsQuick
Aliases: arrayWeightsQuick
Keywords: regression
Description: Array Quality Weights
URL: ../../../library/limma/html/arrayWeightsQuick.html

Entry: asMatrixWeights
Aliases: asMatrixWeights
Keywords: hplot
Description: asMatrixWeights
URL: ../../../library/limma/html/asMatrixWeights.html

Entry: as.data.frame
Aliases: as.data.frame.MArrayLM
Keywords: array
Description: Turn a Microarray Linear Model Object into a Dataframe
URL: ../../../library/limma/html/asdataframe.html

Entry: as.MAList
Aliases: as.MAList
Keywords: classes data
Description: Convert marrayNorm Object to an MAList Object
URL: ../../../library/limma/html/asmalist.html

Entry: as.matrix
Aliases: as.matrix.RGList as.matrix.MAList as.matrix.EListRaw as.matrix.EList as.matrix.MArrayLM as.matrix.marrayNorm as.matrix.PLMset as.matrix.ExpressionSet as.matrix.LumiBatch as.matrix.vsn
Keywords: array
Description: Turn a Microarray Data Object into a Matrix
URL: ../../../library/limma/html/asmatrix.html

Entry: auROC
Aliases: auROC
Keywords: htest
Description: Area Under Receiver Operating Curve
URL: ../../../library/limma/html/auROC.html

Entry: avedups
Aliases: avedups avedups.default avedups.MAList
Keywords: array
Description: Average Over Duplicate Spots
URL: ../../../library/limma/html/avedups.html

Entry: avereps
Aliases: avereps avereps.default avereps.MAList
Keywords: array
Description: Average Over Irregular Replicate Spots
URL: ../../../library/limma/html/avereps.html

Entry: backgroundCorrect
Aliases: backgroundCorrect
Keywords: models
Description: Correct Intensities for Background
URL: ../../../library/limma/html/backgroundcorrect.html

Entry: blockDiag
Aliases: blockDiag
Keywords: array
Description: Block Diagonal Matrix
URL: ../../../library/limma/html/blockDiag.html

Entry: bwss
Aliases: bwss
Keywords: models
Description: Between and within sums of squares
URL: ../../../library/limma/html/bwss.html

Entry: bwss.matrix
Aliases: bwss.matrix
Keywords: models
Description: Between and within sums of squares for matrix
URL: ../../../library/limma/html/bwss.matrix.html

Entry: cbind
Aliases: cbind.RGList cbind.MAList cbind.EList cbind.EListRaw rbind.RGList rbind.MAList rbind.EList rbind.EListRaw
Keywords: manip
Description: Combine RGList, MAList, EList or EListRaw Objects
URL: ../../../library/limma/html/cbind.html

Entry: changeLog
Aliases: changeLog
Keywords: documentation
Description: Limma Change Log
URL: ../../../library/limma/html/changelog.html

Entry: designI2M
Aliases: designI2M designI2A
Keywords: regression
Description: Convert Individual Channel Design Matrix to M-A Format
URL: ../../../library/limma/html/channel2M.html

Entry: classifyTests
Aliases: FStat classifyTestsF classifyTestsT classifyTestsP
Keywords: htest
Description: Multiple Testing Genewise Across Contrasts
URL: ../../../library/limma/html/classifytests.html

Entry: contrasts.fit
Aliases: contrasts.fit
Keywords: htest
Description: Compute Contrasts from Linear Model Fit
URL: ../../../library/limma/html/contrasts.fit.html

Entry: controlStatus
Aliases: controlStatus
Keywords: IO
Description: Set Status of each Spot from List of Spot Types
URL: ../../../library/limma/html/controlStatus.html

Entry: convest
Aliases: convest
Keywords: htest
Description: Estimate Proportion of True Null Hypotheses
URL: ../../../library/limma/html/convest.html

Entry: decideTests
Aliases: decideTests
Keywords: htest
Description: Multiple Testing Across Genes and Contrasts
URL: ../../../library/limma/html/decideTests.html

Entry: dim
Aliases: dim.RGList dim.MAList dim.EListRaw dim.EList dim.MArrayLM length.RGList length.MAList length.EListRaw length.EList length.MArrayLM
Keywords: array
Description: Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
URL: ../../../library/limma/html/dim.html

Entry: dimnames
Aliases: dimnames.RGList dimnames.MAList dimnames.EListRaw dimnames.EList dimnames.MArrayLM dimnames<-.RGList dimnames<-.MAList dimnames<-.EList dimnames<-.EListRaw
Keywords: array
Description: Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
URL: ../../../library/limma/html/dimnames.html

Entry: dupcor
Aliases: duplicateCorrelation
Keywords: multivariate
Description: Correlation Between Duplicates
URL: ../../../library/limma/html/dupcor.html

Entry: ebayes
Aliases: ebayes eBayes treat
Keywords: htest
Description: Empirical Bayes Statistics for Differential Expression
URL: ../../../library/limma/html/ebayes.html

Entry: exprs.MA
Aliases: exprs.MA
Keywords: array
Description: Extract Log-Expression Matrix from MAList
URL: ../../../library/limma/html/exprsMA.html

Entry: fitFDist
Aliases: fitFDist
Keywords: distribution
Description: Moment Estimation of Scaled F-Distribution
URL: ../../../library/limma/html/fitfdist.html

Entry: fitted.MArrayLM
Aliases: fitted.MArrayLM
Keywords: models regression
Description: Fitted Values Method for MArrayLM Fits
URL: ../../../library/limma/html/fitted.MArrayLM.html

Entry: geneSetTest
Aliases: geneSetTest barcodeplot
Keywords: htest
Description: Gene Set Test
URL: ../../../library/limma/html/geneSetTest.html

Entry: getEAWP
Aliases: getEAWP
Keywords: array
Description: Extract Basic Data from Microarray Data Objects
URL: ../../../library/limma/html/getEAWP.html

Entry: getSpacing
Aliases: getSpacing
Keywords: IO
Description: Get Numerical Spacing
URL: ../../../library/limma/html/getSpacing.html

Entry: getLayout
Aliases: getLayout getLayout2 getDupSpacing
Keywords: IO
Description: Extract the Print Layout of an Array from the GAL File
URL: ../../../library/limma/html/getlayout.html

Entry: gls.series
Aliases: gls.series
Keywords: models regression
Description: Fit Linear Model to Microarray Data by Generalized Least Squares
URL: ../../../library/limma/html/gls.series.html

Entry: gridr
Aliases: gridr gridc spotr spotc
Keywords: IO
Description: Row and Column Positions on Microarray
URL: ../../../library/limma/html/gridspotrc.html

Entry: heatdiagram
Aliases: heatdiagram heatDiagram
Keywords: hplot
Description: Stemmed Heat Diagram
URL: ../../../library/limma/html/heatdiagram.html

Entry: helpMethods
Aliases: helpMethods
Keywords: methods
Description: Prompt for Method Help Topics
URL: ../../../library/limma/html/helpMethods.html

Entry: imageplot
Aliases: imageplot
Keywords: hplot
Description: Image Plot of Microarray Statistics
URL: ../../../library/limma/html/imageplot.html

Entry: imageplot3by2
Aliases: imageplot3by2
Keywords: hplot
Description: Write Imageplots to Files
URL: ../../../library/limma/html/imageplot3by2.html

Entry: intraspotCorrelation
Aliases: intraspotCorrelation
Keywords: multivariate
Description: Intra-Spot Correlation for Two Color Data
URL: ../../../library/limma/html/intraspotCorrelation.html

Entry: is.fullrank
Aliases: is.fullrank nonEstimable
Keywords: algebra
Description: Check for Full Column Rank
URL: ../../../library/limma/html/isfullrank.html

Entry: isNumeric
Aliases: isNumeric
Keywords: programming
Description: Test for Numeric Argument
URL: ../../../library/limma/html/isnumeric.html

Entry: kooperberg
Aliases: kooperberg
Keywords: models
Description: Kooperberg Model-Based Background Correction
URL: ../../../library/limma/html/kooperberg.html

Entry: limmaUsersGuide
Aliases: limmaUsersGuide
Keywords: documentation
Description: View Limma User's Guide
URL: ../../../library/limma/html/limmaUsersGuide.html

Entry: lm.series
Aliases: lm.series
Keywords: models regression
Description: Fit Linear Model to Microrray Data by Ordinary Least Squares
URL: ../../../library/limma/html/lm.series.html

Entry: lmFit
Aliases: lmFit
Keywords: models regression
Description: Linear Model for Series of Arrays
URL: ../../../library/limma/html/lmFit.html

Entry: lmscFit
Aliases: lmscFit
Keywords: models regression
Description: Fit Linear Model to Individual Channels of Two-Color Data
URL: ../../../library/limma/html/lmscFit.html

Entry: loessFit
Aliases: loessFit
Keywords: models
Description: Fast Simple Loess
URL: ../../../library/limma/html/loessfit.html

Entry: ma3x3
Aliases: ma3x3.matrix ma3x3.spottedarray
Keywords: smooth
Description: Two dimensional Moving Averages with 3x3 Window
URL: ../../../library/limma/html/ma3x3.html

Entry: makeContrasts
Aliases: makeContrasts
Keywords: regression
Description: Construct Matrix of Custom Contrasts
URL: ../../../library/limma/html/makeContrasts.html

Entry: makeUnique
Aliases: makeUnique
Keywords: character
Description: Make Values of Character Vector Unique
URL: ../../../library/limma/html/makeunique.html

Entry: MAList-class
Aliases: MAList-class
Keywords: classes data
Description: M-value, A-value Expression List - class
URL: ../../../library/limma/html/malist.html

Entry: MArrayLM-class
Aliases: MArrayLM-class
Keywords: classes regression
Description: Microarray Linear Model Fit - class
URL: ../../../library/limma/html/marraylm.html

Entry: mdplot
Aliases: mdplot
Keywords: hplot
Description: mdplot
URL: ../../../library/limma/html/mdplot.html

Entry: merge
Aliases: merge.RGList merge.MAList
Keywords: manip
Description: Merge RGList or MAList Data Objects
URL: ../../../library/limma/html/merge.html

Entry: mergeScans
Aliases: mergeScans mergeScansRG
Keywords: models
Description: Merge two scans of two-color arrays
URL: ../../../library/limma/html/mergeScansRG.html

Entry: modelMatrix
Aliases: modelMatrix uniqueTargets
Keywords: regression
Description: Construct Design Matrix
URL: ../../../library/limma/html/modelMatrix.html

Entry: modifyWeights
Aliases: modifyWeights
Keywords: hplot
Description: modifyWeights
URL: ../../../library/limma/html/modifyWeights.html

Entry: mrlm
Aliases: mrlm
Keywords: models regression
Description: Fit Linear Model to Microrray Data by Robust Regression
URL: ../../../library/limma/html/mrlm.html

Entry: normalizeMedianAbsValues
Aliases: normalizeMedianAbsValues
Keywords: array
Description: Normalize Columns of a Matrix to have the Median Absolute Value
URL: ../../../library/limma/html/normalizeMedianAbsValues.html

Entry: normalizeRobustSpline
Aliases: normalizeRobustSpline
Keywords: models
Description: Normalize Single Microarray Using Shrunk Robust Splines
URL: ../../../library/limma/html/normalizeRobustSpline.html

Entry: normalizeWithinArrays
Aliases: normalizeWithinArrays MA.RG RG.MA
Keywords: models
Description: Normalize Within Arrays
URL: ../../../library/limma/html/normalizeWithinArrays.html

Entry: normalizeBetweenArrays
Aliases: normalizeBetweenArrays
Keywords: models multivariate
Description: Normalize Between Arrays
URL: ../../../library/limma/html/normalizebetweenarrays.html

Entry: normalizeForPrintorder
Aliases: normalizeForPrintorder normalizeForPrintorder.rg plotPrintorder
Keywords: models
Description: Print-Order Normalization
URL: ../../../library/limma/html/normalizeprintorder.html

Entry: normalizeQuantiles
Aliases: normalizeQuantiles
Keywords: models
Description: Normalize Columns of a Matrix to have the same Quantiles
URL: ../../../library/limma/html/normalizequantiles.html

Entry: normexp.fit
Aliases: normexp.fit
Keywords: models
Description: Fit Normal+Exp Convolution Model to Observed Intensities
URL: ../../../library/limma/html/normexpfit.html

Entry: normexp.signal
Aliases: normexp.signal
Keywords: models
Description: Expected Signal Given Observed Foreground Under Normal+Exp Model
URL: ../../../library/limma/html/normexpsignal.html

Entry: plotDensities
Aliases: plotDensities
Keywords: hplot
Description: Individual-channel Densities Plot
URL: ../../../library/limma/html/plotDensities.html

Entry: plotFB
Aliases: plotFB
Keywords: hplot
Description: FB-Plot
URL: ../../../library/limma/html/plotFB.html

Entry: plotMDS
Aliases: plotMDS
Keywords: hplot
Description: Multidimensional scaling plot of microarray data
URL: ../../../library/limma/html/plotMDS.html

Entry: plotSA
Aliases: plotSA
Keywords: hplot
Description: Sigma vs A plot for microarray linear model
URL: ../../../library/limma/html/plotSA.html

Entry: plotlines
Aliases: plotlines
Keywords: hplot
Description: plotlines
URL: ../../../library/limma/html/plotlines.html

Entry: plotMA
Aliases: plotMA
Keywords: hplot
Description: MA-Plot
URL: ../../../library/limma/html/plotma.html

Entry: plotMA3by2
Aliases: plotMA3by2
Keywords: hplot
Description: Write MA-Plots to Files
URL: ../../../library/limma/html/plotma3by2.html

Entry: plotPrintTipLoess
Aliases: plotPrintTipLoess
Keywords: hplot
Description: MA Plots by Print-Tip Group
URL: ../../../library/limma/html/plotprinttiploess.html

Entry: poolVar
Aliases: poolVar
Keywords: htest
Description: Pool Sample Variances with Unequal Variances
URL: ../../../library/limma/html/poolvar.html

Entry: printHead
Aliases: printHead
Keywords: hplot
Description: Print Leading Rows of Large Objects
URL: ../../../library/limma/html/printHead.html

Entry: printorder
Aliases: printorder
Keywords: IO
Description: Identify Order in which Spots were Printed
URL: ../../../library/limma/html/printorder.html

Entry: printtipWeights
Aliases: printtipWeights printtipWeightsSimple
Keywords: regression models
Description: Sub-array Quality Weights
URL: ../../../library/limma/html/printtipWeights.html

Entry: protectMetachar
Aliases: protectMetachar
Keywords: character
Description: Protect Metacharacters
URL: ../../../library/limma/html/protectMetachar.html

Entry: qqt
Aliases: qqt
Keywords: distribution
Description: Student's t Quantile-Quantile Plot
URL: ../../../library/limma/html/qqt.html

Entry: QualityWeights
Aliases: QualityWeights wtarea wtflags wtIgnore.Filter
Keywords: regression
Description: Spot Quality Weights
URL: ../../../library/limma/html/qualwt.html

Entry: read.columns
Aliases: read.columns
Keywords: file
Description: Read specified columns from a file
URL: ../../../library/limma/html/read.columns.html

Entry: read.maimages
Aliases: read.maimages read.imagene
Keywords: file
Description: Read RGList or EListRaw from Image Analysis Output Files
URL: ../../../library/limma/html/read.maimages.html

Entry: readHeader
Aliases: readGenericHeader readGPRHeader readSMDHeader
Keywords: file
Description: Read Header Information from Image Analysis Raw Data File
URL: ../../../library/limma/html/readGPRHeader.html

Entry: readImaGeneHeader
Aliases: readImaGeneHeader
Keywords: file
Description: Read ImaGene Header Information
URL: ../../../library/limma/html/readImaGeneHeader.html

Entry: readSpotTypes
Aliases: readSpotTypes
Keywords: IO
Description: Read Spot Types File
URL: ../../../library/limma/html/readSpotTypes.html

Entry: readTargets
Aliases: readTargets
Keywords: IO
Description: Read Targets File
URL: ../../../library/limma/html/readTargets.html

Entry: readGAL
Aliases: readGAL
Keywords: IO
Description: Read a GAL file
URL: ../../../library/limma/html/readgal.html

Entry: removeBatchEffect
Aliases: removeBatchEffect
Keywords: regression
Description: Remove Batch Effect
URL: ../../../library/limma/html/removeBatchEffect.html

Entry: removeExt
Aliases: removeExt
Keywords: character file
Description: Remove Common Extension from File Names
URL: ../../../library/limma/html/removeext.html

Entry: residuals.MArrayLM
Aliases: residuals.MArrayLM
Keywords: models regression
Description: Extract Residuals from MArrayLM Fit
URL: ../../../library/limma/html/residuals.MArrayLM.html

Entry: RGList-class
Aliases: RGList-class coerce,RGList,exprSet2-method
Keywords: classes data
Description: Red, Green Intensity List - class
URL: ../../../library/limma/html/rglist.html

Entry: roast
Aliases: roast
Keywords: htest
Description: Rotation Gene Set Tests
URL: ../../../library/limma/html/roast.html

Entry: romer
Aliases: romer
Keywords: htest
Description: Rotation Gene Set Enrichment Analysis
URL: ../../../library/limma/html/romer.html

Entry: selectModel
Aliases: selectModel
Keywords: models regression
Description: Select Appropriate Linear Model
URL: ../../../library/limma/html/selectmodel.html

Entry: squeezeVar
Aliases: squeezeVar
Keywords: htest
Description: Smooth Sample Variances
URL: ../../../library/limma/html/squeezeVar.html

Entry: strsplit2
Aliases: strsplit2
Keywords: character
Description: Split Composite Names
URL: ../../../library/limma/html/strsplit2.html

Entry: subsetting
Aliases: [.RGList [.MAList [.EListRaw [.EList [.MArrayLM
Keywords: manip
Description: Subset RGList, MAList, EList or MArrayLM Objects
URL: ../../../library/limma/html/subsetting.html

Entry: summary
Aliases: summary.RGList summary.MAList summary.EListRaw summary.EList summary.MArrayLM
Keywords: methods
Description: Summaries of Microarray Data Objects
URL: ../../../library/limma/html/summary.html

Entry: symbols2indices
Aliases: symbols2indices
Keywords: 
Description: Make Gene Set Indices from Symbols
URL: ../../../library/limma/html/symbols2indices.html

Entry: targetsA2C
Aliases: targetsA2C array2channel
Keywords: htest
Description: Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
URL: ../../../library/limma/html/targetsA2C.html

Entry: tmixture
Aliases: tmixture.vector tmixture.matrix
Keywords: htest
Description: Estimate Scale Factor in Mixture of t-Distributions
URL: ../../../library/limma/html/tmixture.html

Entry: toptable
Aliases: toptable topTable topTableF topTreat
Keywords: htest
Description: Table of Top Genes from Linear Model Fit
URL: ../../../library/limma/html/toptable.html

Entry: trigammaInverse
Aliases: trigammaInverse
Keywords: math
Description: Inverse Trigamma Function
URL: ../../../library/limma/html/trigammainverse.html

Entry: trimWhiteSpace
Aliases: trimWhiteSpace
Keywords: character
Description: Trim Leading and Trailing White Space
URL: ../../../library/limma/html/trimWhiteSpace.html

Entry: uniquegenelist
Aliases: uniquegenelist
Keywords: array
Description: Eliminate Duplicate Names from the Gene List
URL: ../../../library/limma/html/uniquegenelist.html

Entry: unwrapdups
Aliases: unwrapdups
Keywords: array
Description: Unwrap Duplicate Spot Values from Rows into Columns
URL: ../../../library/limma/html/unwrapdups.html

Entry: venn
Aliases: vennCounts vennDiagram
Keywords: htest
Description: Venn Diagrams
URL: ../../../library/limma/html/venn.html

Entry: volcanoplot
Aliases: volcanoplot
Keywords: hplot
Description: Volcano Plot
URL: ../../../library/limma/html/volcanoplot.html

Entry: weighted.median
Aliases: weighted.median
Keywords: univar
Description: Weighted Median
URL: ../../../library/limma/html/weightedmedian.html

Entry: write.fit
Aliases: write.fit
Keywords: IO
Description: Write MArrayLM Object to a File
URL: ../../../library/limma/html/writefit.html

Entry: zscore
Aliases: zscoreGamma zscoreT tZscore
Keywords: distribution
Description: Z-score Equivalents
URL: ../../../library/limma/html/zscore.html