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 1.8.0 Index]