Linear Models for Microarray Data


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Documentation for package `limma' version 2.4.7

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A B C D E F G H I K L M N P Q R S T U V W Z misc

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

-- A --

a.spot Extract M or A-values from SPOT data.frame or matrix
anova.MAList ANOVA Table - method
array2channel Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
arrayWeights Array Quality Weights
arrayWeightsQuick Array Quality Weights
arrayWeightsSimple Array Quality Weights
as.data.frame.MArrayLM Turn a Microarray Linear Model Object into a Dataframe
as.MAList Convert marrayNorm Object to an MAList Object
as.matrix.exprSet Turn a Microarray Data Object into a Matrix
as.matrix.MAList Turn a Microarray Data Object into a Matrix
as.matrix.MArrayLM Turn a Microarray Data Object into a Matrix
as.matrix.marrayNorm Turn a Microarray Data Object into a Matrix
as.matrix.RGList Turn a Microarray Data Object into a Matrix
auROC Area Under Receiver Operating Curve

-- B --

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

-- C --

cbind.MAList Combine RGList or MAList Objects
cbind.RGList Combine RGList or MAList Objects
changeLog Limma Change Log
classifyTestsF Multiple Testing Genewise Across Contrasts
classifyTestsP Multiple Testing Genewise Across Contrasts
classifyTestsT Multiple Testing Genewise Across Contrasts
coerce,RGList,exprSet2-method Red, Green Intensity List - class
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

-- D --

decideTests Multiple Testing Across Genes and Contrasts
designI2A Convert Individual Channel Design Matrix to M-A Format
designI2M Convert Individual Channel Design Matrix to M-A Format
dim.MAList Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.MArrayLM Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dim.RGList Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
dimnames.MAList Retrieve the Dimension Names of an RGList, MAList or MArrayLM Object
dimnames.MArrayLM Retrieve the Dimension Names 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

-- E --

eBayes Empirical Bayes Statistics for Differential Expression
ebayes Empirical Bayes Statistics for Differential Expression
exprSet2-class Expression Set - class

-- F --

fitFDist Moment Estimation of Scaled F-Distribution
fitted.MArrayLM Fitted Values Method for MArrayLM Fits
FStat Multiple Testing Genewise Across Contrasts

-- G --

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
getLayout2 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
gridc Row and Column Positions on Microarray
gridr Row and Column Positions on Microarray

-- H --

heatDiagram Stemmed Heat Diagram
heatdiagram Stemmed Heat Diagram
helpMethods Prompt for Method Help Topics

-- I --

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

-- K --

kooperberg Kooperberg Model-Based Background Correction

-- L --

LargeDataObject-class Large Data Object - class
length.MAList Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.MArrayLM Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
length.RGList Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
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 --

m.spot Extract M or A-values from SPOT data.frame or matrix
MA.RG Normalize Within Arrays
ma3x3.matrix Two dimensional Moving Averages with 3x3 Window
ma3x3.spottedarray Two dimensional Moving Averages with 3x3 Window
makeContrasts Construct Matrix of Custom Contrasts
makeUnique Make Values of Character Vector Unique
MAList-class M-value, A-value Expression List - class
MArrayLM-class Microarray Linear Model Fit - class
matvec Multiply a Matrix by a Vector
mdplot mdplot
merge.MAList Merge RGList or MAList Data Objects
merge.RGList Merge RGList or MAList Data Objects
modelMatrix Construct Design Matrix
modifyWeights modifyWeights
mrlm Fit Linear Model to Microrray Data by Robust Regression

-- N --

nonEstimable Check for Full Column Rank
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.grad Normal + Exponential Log-Likelihood
normexp.m2loglik Normal + Exponential Log-Likelihood
normexp.signal Expected Signal Given Observed Foreground Under Normal+Exp Model

-- P --

plotDensities Individual-channel Densities Plot
plotMA MA-Plot
plotMA3by2 Write MA-Plots to Files
plotPrintorder Print-Order Normalization
plotPrintTipLoess MA Plots by Print-Tip Group
poolVar Pool Sample Variances with Unequal Variances
printHead Print Leading Rows of Large Objects
PrintLayout-class Print Layout - class
printorder Identify Order in which Spots were Printed
protectMetachar Protect Metacharacters

-- Q --

qqt Student's t Quantile-Quantile Plot
QualityWeights Spot Quality Weights

-- R --

rbind.MAList Combine RGList or MAList Objects
rbind.RGList Combine RGList or MAList Objects
read.imagene Read RGList from Image Analysis Output Files
read.maimages Read RGList from Image Analysis Output Files
read.matrix Read Matrix with Headers from File
read.series Read series of image files
readBlueFuseHeader Read Header Information from Image Analysis Raw Data File
readGAL Read a GAL file
readGPRHeader Read Header Information from Image Analysis Raw Data File
readImaGeneHeader Read ImaGene Header Information
readSMDHeader Read Header Information from Image Analysis Raw Data File
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.MA Normalize Within Arrays
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
RGList-class Red, Green Intensity List - class
rlm.series Fit Linear Model to Microrray Data by Robust Regression

-- S --

show,LargeDataObject-method Large Data Object - class
show,TestResults-method Matrix of Test Results - class
splitName Split Composite Gene Names
spotc Row and Column Positions on Microarray
spotr Row and Column Positions on Microarray
squeezeVar Smooth Sample Variances
summary.MAList Summaries of Microarray Data Objects
summary.MArrayLM Summaries of Microarray Data Objects
summary.RGList Summaries of Microarray Data Objects
summary.TestResults Matrix of Test Results - class

-- T --

targetsA2C Convert Two-Color Targets Dataframe from One-Row-Per-Array to One-Row-Per-Channel
TestResults-class Matrix of Test Results - class
tmixture.matrix Estimate Scale Factor in Mixture of t-Distributions
tmixture.vector Estimate Scale Factor in Mixture of t-Distributions
topTable Table of Top Genes from Linear Model Fit
toptable Table of Top Genes from Linear Model Fit
trigammaInverse Inverse Trigamma Function
trimWhiteSpace Trim Leading and Trailing White Space
tZscore Z-score Equivalents

-- U --

uniquegenelist Eliminate Duplicate Names from the Gene List
uniqueTargets Construct Design Matrix
unwrapdups Unwrap Duplicate Spot Values from Rows into Columns

-- V --

vecmat Multiply a Matrix by a Vector
vennCounts Venn Diagrams
vennDiagram Venn Diagrams
volcanoplot Volcano Plot

-- W --

weighted.median Weighted Median
write.fit Write MArrayLM Object to a File
wtarea Spot Quality Weights
wtflags Spot Quality Weights
wtIgnore.Filter Spot Quality Weights
wtVariables Read RGList from Image Analysis Output Files

-- Z --

zscoreGamma Z-score Equivalents
zscoreT Z-score Equivalents

-- misc --

[.MAList Subset RGList, MAList or MArrayLM Objects
[.MArrayLM Subset RGList, MAList or MArrayLM Objects
[.RGList Subset RGList, MAList or MArrayLM Objects