Linear Models for Microarray Data


[Package List] [Top]

Documentation for package `limma' version 1.6.7

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