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]