EnrichmentBrowser (version 1.0.3)

plots: Visualization of gene expression

Description

Visualization of differential gene expression via heatmaps, p-value histograms and volcano plots (fold change vs. p-value).

Usage

pdistr(eset, out.file=NULL, use.adjp=TRUE) volcano(eset, out.file=NULL) exprs.heatmap(eset, out.file=NULL)

Arguments

eset

Expression set. An object of class 'ExpressionSet' containing the gene expression set. See 'read.eset' and 'probe.2.gene.eset' for required annotations in the pData and fData slot.

use.adjp

Logical. Use differential expression p-values that are already corrected for multiple testing? Defaults to TRUE.

out.file

Optional output file to which graphics are plotted to.

Value

None, plots to a graphics device.

See Also

heatmap, truehist

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")
    eset <- read.eset(exprs.file, pdat.file, fdat.file)

    # (2) plot
    exprs.heatmap(eset)
    pdistr(eset)
    volcano(eset)