# Linear Models for Microarray Data

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

1.Introduction | Introduction to the LIMMA Package
2.Classes | Classes Defined by this Package
3.ReadingData | Reading Microarray Data from Files
4.Normalization | Normalization of Microarray Data
5.LinearModels | Linear Models for Microarrays
6.SingleChannel | Single Channel Analysis of Two-Color Microarrays
7.Diagnostics | Diagnostics and Quality Assessment
8.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 File to One-Row-Per-Channel
as.MAList | Convert marrayNorm Object to an MAList Object
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
classifyTests | Treat Simultaneous T-Tests as Classification Problem
classifyTestsF | Treat Simultaneous T-Tests as Classification Problem
classifyTestsP | Treat Simultaneous T-Tests as Classification Problem
classifyTestsT | Treat Simultaneous T-Tests as Classification Problem
coerce,RGList,exprSet2-method | Red, Green Intensity List - class
contrasts.fit | Contrast Information from Linear Model Fit
controlStatus | Set Status of each Spot from List of Spot Types

## -- D --

designMatrix | Construct Design Matrix
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
dupcor.series | Correlation Between Duplicates
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
FStat | Treat Simultaneous T-Tests as Classification Problem

## -- G --

getLayout | Extract the Print Layout of an Array from the GAL File
getSpacing | Get Numerical Spacing
gls.series | Generalized Least Squares for Series of Microarrays
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
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
limmaguideURL | File Location of html Limma User's Guide
lm.series | Linear Model for Series of Arrays
lmFit | Linear Model for Series of Arrays
lmscFit | Single Channel Linear Model for Series of Arrays
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
merge.MAList | Merge RGList or MAList Data Objects
merge.RGList | Merge RGList or MAList Data Objects
modelMatrix | Construct Design Matrix
modifyWeights | modifyWeights

## -- N --

normalizeBetweenArrays | Normalize Between Arrays
normalizeForPrintorder | Print-Order Normalization
normalizeMedianDeviations | Normalize Columns of a Matrix to have the Same Scale
normalizeMedians | Normalize Columns of a Matrix to have the Same Scale
normalizeQuantiles | Normalize Columns of a Matrix to have the same Quantiles
normalizeRobustSpline | Normalize Single Microarray Using Shrunk Robust Splines
normalizeWithinArrays | Normalize Within Arrays

## -- P --

plotDensities | Single-channel Densities Plot
plotMA | MA-Plot
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

## -- 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
readGAL | Read a GAL file
readGPRHeaders | Read GenePix Results File Header Information
readImageneHeaders | Read Imagene Header Information
readSpotTypes | Read Spot Types File
readTargets | Read RNA Targets File
removeExt | Remove Common Extension from File Names
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 | Robust Linear Model for Series of Microarrays

## -- 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.TestResults | Matrix of Test Results - class

## -- T --

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

## -- 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

## -- W --

write.fit | Write MArrayLM Object to a File
wtarea | Spot Quality Weights
wtflags | Spot Quality Weights
wtIgnore.Filter | Spot Quality Weights

## -- Z --

zscoreGamma | z-score equivalents
zscoreT | z-score equivalents

## -- misc --

[.MAList | Subset RGList or MAList Objects
[.RGList | Subset RGList or MAList Objects