plotMA.beads {beadarray} | R Documentation

## Show MA plots

### Description

Function to show an MA plot between two specified samples given by different SAMs or the red and green channels of the same sample.

If two array indices are given then the MA plot will be between the two arrays, otherwise the two channels of one array will be plotted.

### Usage

    plotMA.beads(BSData, array1, array2 = 0, identify = FALSE, label =
    FALSE, highlight = NULL, log = TRUE, main = NULL,ma.ylim=2, sampleSize = NULL, ...)

### Arguments

`BSData` | BeadSummaryList object
`array1` | numeric value to specify the first sample to be plotted
`array2` | numeric value to specify the second sample to be plotted (optional)
`identify` | if TRUE the user will be able to click on points on the plot and bring up useful information, such as ProbeID, gene information etc
`label` | if TRUE the control types for the experiment will be displayed on the plot
`highlight` | vector of numeric values specifying any ProbeIDs which the user wishes to be highlighted on the plot
`log` | if TRUE then a log2 transformation will be applied to the data before plotting
`main` | specifies a title to be written on the plot
`ma.ylim` | specifies the limits for the y axis (M) of the MA plot. Default is 2
`sampleSize` | number of genes to plot. Default is NULL, which plots everything
`...` | other graphical parameters to plot that can be specified

### Details

In the usual way, M is labelled on the y axis and represents the difference between two genes in different samples where as A is the average of the two samples.

Control information must be supplied in a controlTypes vector beforehand.

### Value

MA plot is displayed on current graphical device.

### Author(s)

Mark Dunning

[Package beadarray version 1.0.0 Index]