plotDensity.AffymetrixCelFile

AffymetrixCelFile.plotDensity

plotDensity,AffymetrixCelFile-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=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of <code><a href="/link/double?package=aroma.affymetrix&version=2.5.0&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.numeric?package=aroma.affymetrix&version=2.5.0&to=aroma.light" rd-options="aroma.light" data-mini-rdoc="aroma.light::plotDensity.numeric">plotDensity.numeric</a></code>.

xlim

xlab,ylab

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 density of the log (base 2) values are
     used, otherwise the non-logged values.

A <code><a href="/link/logical?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::logical">logical</a></code> or a <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.5.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code> object.

verbose

Plots the density of the probe signals on the array.

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.AffymetrixCelFile: Plots the density of the probe signals on the array

Description

Usage

Arguments

Value

See Also