plotMA {limma}R Documentation

MA-Plot

Description

Creates an MA-plot with color coding for various sort of control spots.

Usage

plotMA(MA,array=1,pch=16,status=NULL,
       values=c("gene","blank","buffer","utility","negative","calibration","ratio"),
       col=c("black","yellow","orange","pink","brown","blue","red"),
       cex=c(0.1,0.6,0.6,0.6,0.6,0.6,0.6))

Arguments

MA list with components M containing log-ratios and A containing average intensities
array integer giving the array to be plotted. Corresponds to columns of M and A.
pch vector or list of plotting characters
status character vector giving the control status of each spot on the array. If NULL then subsequent arguments are ignored.
values character vector giving unique values of status corresponding to control states of interest
col vector of colors, of the same length as values
cex numeric vector of the same length as values giving sizes for plot symbols

Details

See points for possible values for pch, col and cex.

Value

A plot is created on the current graphics device.

Author(s)

Gordon Smyth

See Also

An overview of diagnostic functions available in LIMMA is given in 6.Diagnostics.


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