madplot-methods: Array-Array Expression Level Distance Plot

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

Description

A false color display of between arrays distances, computed as the MAD of the M-values of each pair of arrays.

Usage

madplot(x, which = "UnitName", transfo = log2, col = NULL, names = "namepart", sort = FALSE, bmar = NULL, add.legend = FALSE, ...)

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”.
col	vector of colors for plot, length is number of samples.
names	optional vector of sample names.
sort	logical, if TRUE the correlation matrix will be sorted decreasingly.
bmar	optional list for bottom margin and axis label magnification cex.axis.
add.legend	logical, if TRUE then a color bar will be drawn.
...	optional arguments to be passed to plot.

Details

Produces a false color display, i.e. heatmap, of between array distances for slot data for an object of class ExprTreeSet, computed as the MAD of the M-values of each pair of arrays.

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 mdaplot.

For bmar=NULL the default list bmar = list(b=6, cex.axis=1.0) will be used initially. However, both bottom margin and axis label magnification will be adjusted depending on the number of label characters and the number of smaples.

Author(s)

Christian Stratowa

See Also

plotMAD, corplot

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