probe2gene {EnrichmentBrowser}R Documentation

Transformation of probe level expression to gene level expression

Description

Transforms expression data on probe level to gene level expression by summarizing all probes that are annotated to a particular gene.

Usage

probe2gene(probeSE, use.mean = TRUE)

Arguments

probeSE

Probe expression data. An object of class SummarizedExperiment. Make sure that the metadata contains an element named annotation that provides the corresponding ID of a recognized platform such as hgu95av2 (Affymetrix Human Genome U95 chip). This requires that a corresponding .db package exists (see http://www.bioconductor.org/packages/release/BiocViews.html#___ChipName for available chips/packages) and that you have it installed. Alternatively, the mapping from probe to gene can also be defined in the rowData slot via two columns named (i) PROBEID for the platform-specific probe ID, and (ii) ENTREZID for the corresponding NCBI Entrez 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

A SummarizedExperiment on gene level.

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

See Also

readSE for reading expression data from file, deAna for differential expression analysis.

Examples


    # (1) reading the expression data from file
    exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
    cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
    rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
    probeSE <- readSE(exprs.file, cdat.file, rdat.file)
    geneSE <- probe2gene(probeSE)
[Package EnrichmentBrowser version 2.10.11 Index]