calculateLimma {puma} | R Documentation

## 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

### 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))
    }

[Package puma version 3.22.0 Index]