Entry: 1.Introduction
Aliases: 1.Introduction
Keywords: documentation
Description: Introduction to the LIMMA Package
URL: ../../../library/limma/html/1introduction.html

Entry: 2.Classes
Aliases: 2.Classes
Keywords: documentation
Description: Classes Defined by this Package
URL: ../../../library/limma/html/2classes.html

Entry: 3.ReadingData
Aliases: 3.ReadingData
Keywords: documentation
Description: Reading Microarray Data from Files
URL: ../../../library/limma/html/3reading.html

Entry: 4.Normalization
Aliases: 4.Normalization
Keywords: documentation
Description: Normalization of Microarray Data
URL: ../../../library/limma/html/4normalization.html

Entry: 5.LinearModels
Aliases: 5.LinearModels
Keywords: documentation
Description: Linear Models for Microarrays
URL: ../../../library/limma/html/5linearmodels.html

Entry: 6.Diagnostics
Aliases: 6.Diagnostics
Keywords: documentation
Description: Diagnostics and Quality Assessment
URL: ../../../library/limma/html/6diagnostics.html

Entry: anova.MAList-method
Aliases: anova.MAList
Keywords: models
Description: ANOVA Table - method
URL: ../../../library/limma/html/anova-method.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: backgroundCorrect
Aliases: backgroundCorrect
Keywords: models
Description: Correct Intensities for Background
URL: ../../../library/limma/html/backgroundcorrect.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: bwss
Aliases: bwss
Keywords: models
Description: Between and within sums of squares
URL: ../../../library/limma/html/bwss.html

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

Entry: classifyTests
Aliases: classifyTests classifyTestsT classifyTestsP
Keywords: htest
Description: Treat Simultaneous T-Tests as Classification Problem
URL: ../../../library/limma/html/classifytests.html

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

Entry: controlStatus
Aliases: controlStatus
Keywords: IO
Description: Get Spot Status from Spot Types
URL: ../../../library/limma/html/controlStatus.html

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

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

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

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

Entry: exprSet2-class
Aliases: exprSet2-class
Keywords: classes data
Description: Expression Set - class
URL: ../../../library/limma/html/exprset2.html

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

Entry: getLayout
Aliases: getLayout
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: Generalized Least Squares for Series of Microarrays
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: is.fullrank
Aliases: is.fullrank
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: LargeDataObject-class
Aliases: LargeDataObject-class show,LargeDataObject-method
Keywords: classes data
Description: Large Data Object - class
URL: ../../../library/limma/html/LargeDataObject.html

Entry: lm.series
Aliases: lm.series
Keywords: models regression
Description: Linear Model for Series of Arrays
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: loessFit
Aliases: loessFit
Keywords: models
Description: Fast Simple Loess
URL: ../../../library/limma/html/loessfit.html

Entry: m.spot
Aliases: m.spot a.spot
Keywords: IO
Description: Extract M or A-values from SPOT data.frame or matrix
URL: ../../../library/limma/html/m.spot.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: matvec
Aliases: matvec vecmat
Keywords: array algebra
Description: Multiply a Matrix by a Vector
URL: ../../../library/limma/html/matvec.html

Entry: merge.RGList
Aliases: merge.RGList
Keywords: manip
Description: Merge RGList Data Objects
URL: ../../../library/limma/html/merge.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: normalizeRobustSpline
Aliases: normalizeRobustSpline
Keywords: models
Description: Normalize Single Microarray Using Shrunk Robust Splines
URL: ../../../library/limma/html/normalizeRobustSpline.html

Entry: normalizeScale
Aliases: normalizeMedianDeviations normalizeMedians
Keywords: array
Description: Normalize Columns of a Matrix to have the Same Scale
URL: ../../../library/limma/html/normalizescale.html

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

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

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

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

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

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

Entry: printorder
Aliases: printorder
Keywords: IO
Description: Identify Order in which Spots were Printed
URL: ../../../library/limma/html/printorder.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.maimages
Aliases: read.maimages read.imagene
Keywords: file
Description: Read RGList from Image Analysis Output Files
URL: ../../../library/limma/html/read.maimages.html

Entry: read.matrix
Aliases: read.matrix
Keywords: file
Description: Read Matrix with Headers from File
URL: ../../../library/limma/html/read.matrix.html

Entry: read.series
Aliases: read.series
Keywords: file
Description: Read series of image files
URL: ../../../library/limma/html/read.series.html

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

Entry: readGPRHeaders
Aliases: readGPRHeaders
Keywords: file
Description: Read GenePix Results File Header Information
URL: ../../../library/limma/html/readGPRHeaders.html

Entry: readImageneHeaders
Aliases: readImageneHeaders
Keywords: file
Description: Read Imagene Header Information
URL: ../../../library/limma/html/readImageneHeaders.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 RNA Targets File
URL: ../../../library/limma/html/readTargets.html

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

Entry: rg.genepix
Aliases: rg.genepix
Keywords: IO
Description: Extract RGList from data.frames Containing Genepix Data
URL: ../../../library/limma/html/rg.genepix.html

Entry: rg.quantarray
Aliases: rg.quantarray
Keywords: IO
Description: Extract RGList from data.frames Containing Quantarray Data
URL: ../../../library/limma/html/rg.quantarray.html

Entry: rg.series.spot
Aliases: rg.series.spot
Keywords: IO
Description: Read RGList from SPOT Image Analysis Output Files
URL: ../../../library/limma/html/rg.series.spot.html

Entry: rg.spot
Aliases: rg.spot
Keywords: IO
Description: Extract RGList from data.frames Containing SPOT Data
URL: ../../../library/limma/html/rg.spot.html

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

Entry: rlm.series
Aliases: rlm.series
Keywords: models regression
Description: Robust Linear Model for Series of Microarrays
URL: ../../../library/limma/html/rlm.series.html

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

Entry: subsetting
Aliases: [.RGList [.MAList
Keywords: manip
Description: Subset RGList or MAList Objects
URL: ../../../library/limma/html/subsetting.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
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: 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: zscore
Aliases: zscoreGamma zscoreT
Keywords: distribution
Description: z-score equivalents
URL: ../../../library/limma/html/zscore.html
