mvaplot-methods

mvaplot

object of class <code><a rd-options="" href="/link/ExprTreeSet?package=xps&version=1.32.0" data-mini-rdoc="xps::ExprTreeSet">ExprTreeSet</a></code>.

type of probes to be used, for details see <code><a rd-options="" href="/link/validData?package=xps&version=1.32.0" data-mini-rdoc="xps::validData">validData</a></code>.

which

a valid function to transform the data, usually &#147;log2&#148;, or &#147;0&#148;.

transfo

method to compute M, &#147;mean&#148; or &#147;median&#148;.

method

names

ylim

xlab

ylab

an integer specifying a symbol or a character to be used as the default in plotting points.

optional arguments to be passed to <code>plot</code>.

Produce scatter plots of M values vs A values of the samples.Usage<code>
mvaplot(x,
 which = "UnitName",
 transfo = log2,
 method = "median",
 names = "namepart",
 ylim = c(-6,6),
 xlab = "A",
 ylab = "M",
 pch = '.',
 las = 2,
 ...)
</code>

methods

The package handles pre-processing, normalization, filtering
and analysis of Affymetrix GeneChip expression arrays, including exon
arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST)
and plate arrays on computers with 1 GB RAM only. It imports Affymetrix
.CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA,
MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to
XPS (eXpression Profiling System), which is based on ROOT, an object-oriented
framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite
for the usage of this package, however, no knowledge of ROOT is required.
ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

Christian Stratowa

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

mvaplot-methods function

object of class <code><a rd-options='' href='ExprTreeSet'>ExprTreeSet</a></code>.

type of probes to be used, for details see <code><a rd-options='' href='validData'>validData</a></code>.

Produce scatter plots of M values vs A values of the samples.

Usage

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

mvaplot-methods: M vs A Plot

Description

Arguments

Details

See Also