pumaDE {puma}R Documentation

Calculate differential expression between conditions

Description

The function generates lists of genes ranked by probability of differential expression (DE).

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

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

Author(s)

Richard D. Pearson

See Also

Related methods 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 1.2.0 Index]