ArrayExplorer

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

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

ArrayExplorer function

<dl> <dt>csTuple</dt>
<dd>An <code>AffymetrixCelSet</code> object.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Methods: <table class="table">
<tr><td></td><td><code>addColorMap</code></td><td>-</td></tr>
<tr><td></td><td><code>getColorMaps</code></td><td>-</td></tr>
<tr><td></td><td><code>getDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getSetTuple</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChipTypes</code></td><td>-</td></tr>
<tr><td></td><td><code>process</code></td><td>-</td></tr>
<tr><td></td><td><code>setArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>setColorMaps</code></td><td>-</td></tr>
</table>Methods inherited from Explorer: 
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile
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 ArrayExplorer 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>Explorer</code> 
<code>~~~~~~~|</code> 
<code>~~~~~~~+--</code><code>ArrayExplorer</code> 
Directly known subclasses: 
 
public abstract static class ArrayExplorer 
extends Explorer

The ArrayExplorer class — ArrayExplorer

<dl>

 <dt>csTuple</dt>
<dd>An <code>AffymetrixCelSet</code> object.</dd>

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

</dl>

Methods: <table class='table'>
<tr><td></td><td><code>addColorMap</code></td><td>-</td></tr>
<tr><td></td><td><code>getColorMaps</code></td><td>-</td></tr>
<tr><td></td><td><code>getDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getSetTuple</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChipTypes</code></td><td>-</td></tr>
<tr><td></td><td><code>process</code></td><td>-</td></tr>
<tr><td></td><td><code>setArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>setColorMaps</code></td><td>-</td></tr>
</table>



Methods inherited from Explorer: 
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile
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

	`addColorMap`	-
	`getColorMaps`	-
	`getDataSet`	-
	`getSetTuple`	-
	`nbrOfChipTypes`	-
	`process`	-
	`setArrays`	-
	`setColorMaps`	-

ArrayExplorer: The ArrayExplorer class

Description

Usage

Arguments

Fields and Methods

Author