EnrichmentBrowser (version 1.0.3)

probe.2.gene.eset: Transformation of probe level expression to gene level expression

Description

Reads expression data at probe level and summarizes gene expression behavior by averaging over all probes that are annotated to a particular gene. A subsequent differential expression analysis at the gene level is automatically performed.

Usage

probe.2.gene.eset(probe.eset, use.mean=TRUE,   heatm.file=NULL, distr.file=NULL, volc.file=NULL)

Arguments

probe.eset

Probe expression set of class 'ExpressionSet'. The fData slot of the expression set must contain a 'GENE' column that lists for each probe the corresponding KEGG gene ID.

use.mean

Logical. Determining, in case of multiple probes for one gene, whether a mean value is computed or the probe that discriminate the most between the two sample group is kept. Defaults to TRUE.

heatm.file

Optional. If specified, a heatmap is plotted in PNG format to file.

distr.file

Optional. If specified, the p-value distribution is plotted in PNG format to file.

volc.file

Optional. If specified, the volcano plot is plotted in PNG format to file.

Value

An ExpressionSet-class on gene level with measures of differential expression annotated.

See Also

ExpressionSet-class, eBayes, p.adjust

Examples

    # (1) reading the expression data from file
    exprs.file <- system.file("extdata/ALL_exprs.tab", package="EnrichmentBrowser")
    pdat.file <- system.file("extdata/ALL_pData.tab", package="EnrichmentBrowser")
    fdat.file <- system.file("extdata/ALL_fData.tab", package="EnrichmentBrowser")
    probe.eset <- read.eset(exprs.file, pdat.file, fdat.file)
    gene.eset <- probe.2.gene.eset(probe.eset) 
    head(fData(gene.eset))