plotMvsA.AffymetrixCelFile

AffymetrixCelFile.plotMvsA

plotMvsA,AffymetrixCelFile-method

The reference channel, i.e. the denominator in the
    log ratios.

reference

Indices of the probe signals to be plotted.

indices

xlim,ylim

xlab,ylab

Additional arguments passed to <code><a href="/link/plot?package=aroma.affymetrix&version=2.5.0&to=graphics" rd-options="graphics" data-mini-rdoc="graphics::plot">plot</a></code>.

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=2.5.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the plot is annotated with information about
    the data plotted, otherwise not.

annotate

Plots log-ratio versus log-intensity in a scatter plot.

methods

internal

This package implements classes for files and sets of
        files for various Affymetrix file formats, e.g.
        AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
        These are designed to be memory efficient but still being fast.
        The idea is to keep all data on file and only read data into
        memory when needed.  Clever caching mechanisms are used to
        minimize the overhead of data IO.  All of the above is hidden
        in the package API and for the developer (and the end user),
        the data is queried as if it lives in memory.  With this design
        it is only the diskspace that limits the number of arrays that
        can be analyzed.  To install, do:
        source("http://www.aroma-project.org/hbLite.R");
        hbInstall("aroma.affymetrix").

plotMvsA.AffymetrixCelFile: Plots log-ratio versus log-intensity in a scatter plot

Description

Usage

Arguments

Value

See Also