plotDensity.AffymetrixCelFile

AffymetrixCelFile.plotDensity

plotDensity,AffymetrixCelFile-method

Plots the density of the probe signals on the array.

methods

internal

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system.  The only parameter that limits the number of chips that can be processed is the amount of available disk space.  The Aroma Framework has successfully been used in studies to process tens of thousands of arrays.  This package has actively been used since 2006.

Henrik Bengtsson

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

James Bullard

Kasper Hansen

Pierre Neuvial

Elizabeth Purdom

Mark Robinson

Ken Simpson

plotDensity.AffymetrixCelFile function

<dl> <dt>subset</dt>
<dd>The subset of probes to considered before any
 filtering by probe type is applied.
 If a <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code> of <code><a href="/link/double?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::double">double</a></code>s, the cell indices.
 If a scalar <code><a href="/link/double?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::double">double</a></code> in [0,1], the fraction of cells, which can
 be used to speed up the plotting if approximate densities are
 acceptable.
 if <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, all cells are considered.</dd> <dt>types</dt>
<dd>The type of probes to include, e.g. <code>"all"</code>,
 <code>"pmmm"</code>, <code>"pm"</code>, and <code>"mm"</code>.</dd> <dt>...</dt>
<dd>Additional arguments passed to
 <code>plotDensity.numeric</code>.</dd> <dt>xlim</dt>
<dd>The range on the x axis.</dd> <dt>xlab,ylab</dt>
<dd>The labels on the x and the y axes.</dd> <dt>log</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::TRUE">TRUE</a></code>, the density of the log (base 2) values are
 used, otherwise the non-logged values.</dd> <dt>verbose</dt>
<dd>A <code><a href="/link/logical?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::logical">logical</a></code> or a <code>Verbose</code> object.</dd></dl>

Arguments

Author

Plots the density of the probe signals on the array — plotDensity.AffymetrixCelFile

<dl>

 <dt>subset</dt>
<dd>The subset of probes to considered before any
 filtering by probe type is applied.
 If a <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of <code><a href='https://rdrr.io/r/base/double.html'>double</a></code>s, the cell indices.
 If a scalar <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> in [0,1], the fraction of cells, which can
 be used to speed up the plotting if approximate densities are
 acceptable.
 if <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, all cells are considered.</dd>

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

 <dt>...</dt>
<dd>Additional arguments passed to
 <code>plotDensity.numeric</code>.</dd>

 <dt>xlim</dt>
<dd>The range on the x axis.</dd>

 <dt>xlab,ylab</dt>
<dd>The labels on the x and the y axes.</dd>

 <dt>log</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, the density of the log (base 2) values are
 used, otherwise the non-logged values.</dd>

 <dt>verbose</dt>
<dd>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> or a <code>Verbose</code> object.</dd>

</dl>

Plots the density of the probe signals on the array

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

Description

Usage

Value

Arguments

Author

See Also