calculateParametersGsb.AffymetrixCelSet

AffymetrixCelSet.calculateParametersGsb

calculateParametersGsb,AffymetrixCelSet-method

Computes parameters for adjustment of specific binding.

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

calculateParametersGsb.AffymetrixCelSet function

<dl> <dt>nbrOfPms</dt>
<dd>The number of random PMs to use in estimation.</dd> <dt>affinities</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> of probe affinities.</dd> <dt>seed</dt>
<dd>An (optional) <code><a href="/link/integer?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::integer">integer</a></code> specifying a temporary random seed
 to be used during processing. The random seed is set to its original
 state when done. If <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, it is not set.</dd> <dt>...</dt>
<dd>Not used.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

Computes parameters for adjustment of specific binding — calculateParametersGsb.AffymetrixCelSet

<dl>

 <dt>nbrOfPms</dt>
<dd>The number of random PMs to use in estimation.</dd>

 <dt>affinities</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> of probe affinities.</dd>

 <dt>seed</dt>
<dd>An (optional) <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> specifying a temporary random seed
 to be used during processing. The random seed is set to its original
 state when done. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, it is not set.</dd>

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

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

</dl>

Computes parameters for adjustment of specific binding

calculateParametersGsb.AffymetrixCelSet: Computes parameters for adjustment of specific binding

Description

Usage

Arguments

Author

Details