plotDensity.AffymetrixCelSet

AffymetrixCelSet.plotDensity

plotDensity,AffymetrixCelSet-method

The subset of probes to considered <em>before</em> any
    filtering by probe type is applied.
    If a <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of <code><a href="/link/double?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::double">double</a></code>s, the cell indices.
    If 

subset

The type of probes to include, e.g. <code>"all"</code>,
    <code>"pmmm"</code>, <code>"pm"</code>, and <code>"mm"</code>.

types

Additional arguments passed to
     <code><a href="/link/plotDensity.AffymetrixCelFile?package=aroma.affymetrix&version=2.2.0" rd-options="" data-mini-rdoc="aroma.affymetrix::plotDensity.AffymetrixCelFile">plotDensity.AffymetrixCelFile</a></code>().

A <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of colors for each of the arrays.

A <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of line types for each of the arrays.

A <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of line widths for each of the arrays.

If <code><a href="/link/FALSE?package=aroma.affymetrix&version=2.2.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::FALSE">FALSE</a></code>, a new plot is created, otherwise the generated
    graphics is added to the current 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").

plotDensity.AffymetrixCelSet: Plots the densities of all samples

Description

Usage

Arguments

Value

See Also