plotMA {beadarray}R Documentation

Show MA plots

Description

Function which produces an MA plot between two specified arrays.

Usage

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

Arguments

exprs a matrix of expression values
array1 integer specifying the first array to plot
array2 integer specifying the second array to plot
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

The log2 difference in intensity (M-value, log-ratio) are plotted against the log2 average intensity (A-value) for each probe for the two arrays selected.

Value

A smoothed MA scatter plot is displayed on the current graphical device.

Author(s)

Mark Dunning

Examples

data(BSData)

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

[Package beadarray version 1.10.0 Index]