EnrichmentBrowser (version 2.2.2)

plots: Visualization of gene expression

Description

Visualization of differential gene expression via heatmap, p-value histogram and volcano plot (fold change vs. p-value).

Usage

pdistr( p ) volcano( fc, p ) exprs.heatmap( expr, grp )

Arguments

p

Numeric vector of p-values for each gene.

fc

Numeric vector of fold changes (typically on log2 scale).

expr

Expression matrix. Rows correspond to genes, columns to samples.

grp

*BINARY* group assignment for the samples. Use '0' and '1' for unaffected (controls) and affected (cases) samples, respectively.

Value

None, plots to a graphics device.

See Also

de.ana for differential expression analysis, heatmap and truehist for generic plotting.

Examples

    # (1) simulating expression data: 100 genes, 12 samples
    eset <- make.example.data(what="eset") 
    
    # plot heatmap
    exprs.heatmap(expr=exprs(eset), grp=as.factor(pData(eset)$GROUP))

    # (2) DE analysis
    eset <- de.ana(eset)
    pdistr(fData(eset)$ADJ.PVAL)
    volcano(fc=fData(eset)$FC, p=fData(eset)$ADJ.PVAL)