pumaDE {puma}R Documentation

Calculate differential expression between conditions

Description

The function generates lists of genes ranked by probability of differential expression (DE). This uses the PPLR method.

Usage

pumaDE(
        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

A separate list will be created for each contrast of interest.

While it is possible to run this function on data from individual arrays, it is generally recommended that this function is run on the output of the function pumaComb (which combines information from replicates).

Value

An object of class DEResult-class.

Author(s)

Richard D. Pearson

See Also

Related methods calculateLimma, calculateFC, calculateTtest, pumaComb, mmgmos, pplr, 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_mmgmos <- mmgmos(affybatch.example)
        eset_mmgmos_normd <- pumaNormalize(eset_mmgmos)
        eset_comb <- pumaComb(eset_mmgmos_normd)
        esetDE <- pumaDE(eset_comb)
        esetDE$genes[1:6,]
        esetDE$p[1:6,]

[Package puma version 1.2.1 Index]