EnrichmentBrowser (version 2.2.2)

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.

Usage

probe.2.gene.eset( probe.eset, use.mean = TRUE )

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 (use.mean=TRUE), or the probe that discriminate the most between the two sample group is kept (use.mean=FALSE). Defaults to TRUE.

Value

An ExpressionSet on gene level.

See Also

ExpressionSet-class, read.eset for reading expression data from file, de.ana for differential expression analysis.

Examples

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