plotMA: MvA Scatter Plot for Device

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Produce scatter plots of M values vs A values of the samples for the selected device.

Usage

plotMA(x,
       transfo = log2,
       method  = "median",
       names   = "namepart",
       ylim    = c(-6, 6),
       xlab    = "A",
       ylab    = "M",
       pch     = ".",
       mar     = c(3, 3, 2, 1),
       dev     = "screen",
       outfile = "MvAPlot",
       w       = 540,
       h       = 540,
       ...)

Arguments

x	object of class ExprTreeSet.
transfo	a valid function to transform the data, usually “log2”, or “0”.
method	method to compute M, “mean” or “median”.
names	optional vector of sample names.
ylim	range for the plotted M values.
xlab	a title for the x axis.
ylab	a title for the y axis.
pch	either an integer specifying a symbol or a single character to be used in plotting points.
mar	plot margin.
dev	graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.
outfile	the name of the output file.
w	the width of the device in pixels.
h	the height of the device in pixels.
...	optional arguments to be passed to plot.

Details

Produces M vs A plots for slot data for an object of class ExprTreeSet for the selected graphics device.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as M vs A plot.

Author(s)

Christian Stratowa

See Also

mvaplot

xps documentation built on Nov. 8, 2020, 6 p.m.