puma (version 3.12.0)

calculateLimma: 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

eset

An object of class ExpressionSet

design.matrix

A design matrix

contrast.matrix

A contrast matrix

Value

An object of class DEResult.

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.

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))
}