mvaplot-methods: M vs A Plot

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.

Usage

mvaplot(x, which = "UnitName", transfo = log2, method = "median", names = "namepart", ylim = c(-6,6), xlab = "A", ylab = "M", pch = '.', las = 2, ...)

Arguments

x	object of class ExprTreeSet.
which	type of probes to be used, for details see validData.
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 label for the x axis.
ylab	a label for the y axis.
pch	an integer specifying a symbol or a character to be used as the default in plotting points.
las	the style of axis labels.
...	optional arguments to be passed to plot.

Details

Produces mvaplots for slot data for an object of class ExprTreeSet.

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 mvaplot.

Author(s)

Christian Stratowa

See Also

plotMA

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