normalizeQuantile.AffymetrixCelFile

AffymetrixCelFile.normalizeQuantile

normalizeQuantile,AffymetrixCelFile-method

Normalizes the probe intensities to a target empirical distribution.

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

normalizeQuantile.AffymetrixCelFile function

<dl> <dt>path</dt>
<dd>The path where to save the normalized data files.</dd> <dt>xTarget</dt>
<dd>A <code><a href="/link/numeric?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code>. The empirical distribution
 to which all arrays should be normalized to.</dd> <dt>subsetToUpdate</dt>
<dd>The indices of the probes to be updated.
 If <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, all are updated.</dd> <dt>typesToUpdate</dt>
<dd>Types of probes to be updated. For more details,
 see argument <code>types</code> of <code>identifyCells()</code> for the
 <code>AffymetrixCdfFile</code> class.</dd> <dt>...</dt>
<dd>Additional arguments passed to <code>normalizeQuantile()</code>.</dd> <dt>overwrite</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::TRUE">TRUE</a></code>, already normalized arrays are overwritten,
 unless skipped, otherwise an error is thrown.</dd> <dt>skip</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 array is not normalized if it already exists.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

Normalizes the probe intensities to a target empirical distribution — normalizeQuantile.AffymetrixCelFile

<dl>

 <dt>path</dt>
<dd>The path where to save the normalized data files.</dd>

 <dt>xTarget</dt>
<dd>A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code>. The empirical distribution
 to which all arrays should be normalized to.</dd>

 <dt>subsetToUpdate</dt>
<dd>The indices of the probes to be updated.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, all are updated.</dd>

 <dt>typesToUpdate</dt>
<dd>Types of probes to be updated. For more details,
 see argument <code>types</code> of <code>identifyCells()</code> for the
 <code>AffymetrixCdfFile</code> class.</dd>

 <dt>...</dt>
<dd>Additional arguments passed to <code>normalizeQuantile()</code>.</dd>

 <dt>overwrite</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, already normalized arrays are overwritten,
 unless skipped, otherwise an error is thrown.</dd>

 <dt>skip</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, the array is not normalized if it already exists.</dd>

 <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd>

</dl>

Normalizes the probe intensities to a target empirical distribution

normalizeQuantile.AffymetrixCelFile: Normalizes the probe intensities to a target empirical distribution

Description

Usage

Value

Arguments

Author

See Also