Calculate differential expression between conditions using limma

Description

Runs a default analysis using the limma package. Automatically creates design and contrast matrices if not specified. This function is useful for comparing limma results with those of other differential expression (DE) methods such as pumaDE.

Usage

calculateLimma(
	eset
,	design.matrix = createDesignMatrix(eset)
,	contrast.matrix = createContrastMatrix(eset)
)

Arguments

Details

The eset argument must be supplied, and must be a valid ExpressionSet object. Design and contrast matrices can be supplied, but if not, default matrices will be used. These should usually be sufficient for most analyses.

Value

An object of class DEResult.

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, calculateTtest, calculateFC, createDesignMatrix and createContrastMatrix and class DEResult

Examples

if (require(affydata)) {
	data(Dilution)
	eset_rma <- affy:::rma(Dilution)
	#	Next line used so eset_rma only has information about the liver factor
	#	The scanner factor will thus be ignored, and the two arrays of each level
	#	of the liver factor will be treated as replicates
	pData(eset_rma) <- pData(eset_rma)[,1, drop=FALSE]
	limmaRes <- calculateLimma(eset_rma)
	topGeneIDs(limmaRes,numberOfGenes=6)
	plotErrorBars(eset_rma, topGenes(limmaRes))
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(puma)
Loading required package: oligo
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/puma/calculateLimma.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateLimma
> ### Title: Calculate differential expression between conditions using limma
> ### Aliases: calculateLimma
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+ 	data(Dilution)
+ 	eset_rma <- affy:::rma(Dilution)
+ 	#	Next line used so eset_rma only has information about the liver factor
+ 	#	The scanner factor will thus be ignored, and the two arrays of each level
+ 	#	of the liver factor will be treated as replicates
+ 	pData(eset_rma) <- pData(eset_rma)[,1, drop=FALSE]
+ 	limmaRes <- calculateLimma(eset_rma)
+ 	topGeneIDs(limmaRes,numberOfGenes=6)
+ 	plotErrorBars(eset_rma, topGenes(limmaRes))
+ }
Loading required package: affydata
Loading required package: affy

Attaching package: 'affy'

The following objects are masked from 'package:oligo':

    MAplot, intensity, mm, mm<-, mmindex, pm, pm<-, pmindex,
    probeNames, rma

The following object is masked from 'package:oligoClasses':

    list.celfiles

     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Background correcting
Normalizing
Calculating Expression
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:oligo':

    backgroundCorrect

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>