fitQuantileNormFcn.AffymetrixCelFile

AffymetrixCelFile.fitQuantileNormFcn

fitQuantileNormFcn,AffymetrixCelFile-method

Fits quantile normalization functions for the arrays in the data set.

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

fitQuantileNormFcn.AffymetrixCelFile function

<dl> <dt>yTarget</dt>
<dd>The target probe signals.</dd> <dt>subset</dt>
<dd>An optional <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> specifying the indices of the
 subset of probes to be used to fit the normalization function.</dd> <dt>spar, nknots</dt>
<dd>Control parameters passed to
 <code><a href="/link/smooth.spline?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::smooth.spline">smooth.spline</a></code>.</dd> <dt>...</dt>
<dd>Not used.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

Fits quantile normalization functions for the arrays in the data set — fitQuantileNormFcn.AffymetrixCelFile

<dl>

 <dt>yTarget</dt>
<dd>The target probe signals.</dd>

 <dt>subset</dt>
<dd>An optional <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> specifying the indices of the
 subset of probes to be used to fit the normalization function.</dd>

 <dt>spar, nknots</dt>
<dd>Control parameters passed to
 <code><a href='https://rdrr.io/r/stats/smooth.spline.html'>smooth.spline</a></code>.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

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

</dl>

Fits quantile normalization functions for the arrays in the data set

fitQuantileNormFcn.AffymetrixCelFile: Fits quantile normalization functions for the arrays in the data set

Description

Usage

Value

Arguments

Author

See Also