plotMA {beadarray}R Documentation

Show MA plots

Description

Function to show an MA plot between two specified samples from different BeadArrays.

Usage

plotMA(exprs, array1=1, array2=2, genesToLabel=NULL, labelCol="red", foldLine=2, log=TRUE, labelpch=16, ma.ylim=2, sampleSize=NULL,...)

Arguments

exprs expression matrix from an ExpressionSet or eSet
array1 numeric value to specify the first sample to be plotted
array2 numeric value to specify the second sample to be plotted (optional)
genesToLabel vector of genes to highlight on the plot. These must match the rownames of exprs
labelCol plotting colours for highlighted genes
foldLine a numeric value defining where to draw horizontal fold change lines on the plot
log if TRUE the data will be log-transformed before plotting
labelpch plotting characters for highlighted genes
ma.ylim numeric value specifying the range of the plot (from -ma.ylim to ma.ylim)
sampleSize The number of genes to plot. Default is NULL, which plots every gene.
... other graphical parameters to plot that can be specified

Details

On the y axis, the log-2 difference in intensity (M-values) between the two samples is shown and along the x axis, the log-2 average intensity (A-values) are plotted.

Value

MA plot is displayed on current graphical device.

Author(s)

Mark Dunning

Examples

data(BSData)

plotMA(exprs(BSData), array1=1, array2=2)

[Package beadarray version 1.6.0 Index]