QualityAssessmentModel

Package: aroma.affymetrix 
Class QualityAssessmentModel 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>QualityAssessmentModel</code> 
Directly known subclasses: 
 
public static class QualityAssessmentModel 
extends Object

classes

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

QualityAssessmentModel function

<dl> <dt>plm</dt>
<dd>A <code>ProbeLevelModel</code>.</dd> <dt>tags</dt>
<dd>A <code><a href="/link/character?package=aroma.affymetrix&version=3.2.3" data-mini-rdoc="aroma.affymetrix::character">character</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.3" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code> of tags.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Methods: <table class="table">
<tr><td></td><td><code>getChipEffectSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getFullName</code></td><td>-</td></tr>
<tr><td></td><td><code>getName</code></td><td>-</td></tr>
<tr><td></td><td><code>getPath</code></td><td>-</td></tr>
<tr><td></td><td><code>getPlm</code></td><td>-</td></tr>
<tr><td></td><td><code>getResiduals</code></td><td>Calculates the residuals from a probe-level model.</td></tr>
<tr><td></td><td><code>getTags</code></td><td>-</td></tr>
<tr><td></td><td><code>getWeights</code></td><td>Calculates the weights from the robust fit to a probe-level model.</td></tr>
<tr><td></td><td><code>nbrOfArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>plotNuse</code></td><td>-</td></tr>
<tr><td></td><td><code>plotRle</code></td><td>-</td></tr>
</table>Methods inherited from Object: 
$, $&lt;-, [[, [[&lt;-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

Fields and Methods

Author

Package: aroma.affymetrix 
Class QualityAssessmentModel 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>QualityAssessmentModel</code> 
Directly known subclasses: 
 
public static class QualityAssessmentModel 
extends Object

The QualityAssessmentModel class — QualityAssessmentModel

<dl>

 <dt>plm</dt>
<dd>A <code>ProbeLevelModel</code>.</dd>

 <dt>tags</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of tags.</dd>

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

</dl>

Methods: <table class='table'>
<tr><td></td><td><code>getChipEffectSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getFullName</code></td><td>-</td></tr>
<tr><td></td><td><code>getName</code></td><td>-</td></tr>
<tr><td></td><td><code>getPath</code></td><td>-</td></tr>
<tr><td></td><td><code>getPlm</code></td><td>-</td></tr>
<tr><td></td><td><code>getResiduals</code></td><td>Calculates the residuals from a probe-level model.</td></tr>
<tr><td></td><td><code>getTags</code></td><td>-</td></tr>
<tr><td></td><td><code>getWeights</code></td><td>Calculates the weights from the robust fit to a probe-level model.</td></tr>
<tr><td></td><td><code>nbrOfArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>plotNuse</code></td><td>-</td></tr>
<tr><td></td><td><code>plotRle</code></td><td>-</td></tr>
</table>



Methods inherited from Object: 
$, $&lt;-, [[, [[&lt;-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

	`getChipEffectSet`	-
	`getDataSet`	-
	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getPlm`	-
	`getResiduals`	Calculates the residuals from a probe-level model.
	`getTags`	-
	`getWeights`	Calculates the weights from the robust fit to a probe-level model.
	`nbrOfArrays`	-
	`plotNuse`	-
	`plotRle`	-

QualityAssessmentModel: The QualityAssessmentModel class

Description

Usage

Arguments

Fields and Methods

Author