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]