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 pumaDE.

Usage

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

Arguments

eset An object of class ExpressionSet
design.matrix A design matrix
contrast.matrix A contrast matrix
direction A string ("either", "up" or "down")

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

A list with two elements. The first element (p) is a matrix of p-values. Each column represent one contrast. Within each column the p-values are ordered. The second element (genes) is a matrix of row numbers, which can be used to map p-values back to probe sets.

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, createDesignMatrix and createContrastMatrix

Examples

        library(puma)
        data(affybatch.example)
        pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
            , "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
        eset_rma <- rma(affybatch.example)
        limmaRes <- calculateLimma(eset_rma)
        limmaRes$p[1:6]
        plotErrorBars(eset_rma, limmaRes$genes[1])

[Package puma version 1.2.0 Index]