ArrayExplorer

An <code><a rd-options="" href="/link/AffymetrixCelSet?package=aroma.affymetrix&version=3.0.0" data-mini-rdoc="aroma.affymetrix::AffymetrixCelSet">AffymetrixCelSet</a></code> object.

csTuple

Package: aroma.affymetrix 
Class ArrayExplorer<code><a rd-options="R.oo" href="/link/Object?package=aroma.affymetrix&version=3.0.0&to=R.oo" data-mini-rdoc="R.oo::Object">Object</a></code>
<code>~~|</code>
<code>~~+--</code><code><a rd-options="aroma.core" href="/link/Explorer?package=aroma.affymetrix&version=3.0.0&to=aroma.core" data-mini-rdoc="aroma.core::Explorer">Explorer</a></code>
<code>~~~~~~~|</code>
<code>~~~~~~~+--</code><code>ArrayExplorer</code>Directly known subclasses:
public abstract static class ArrayExplorer
extends <a rd-options="aroma.core" href="/link/Explorer?package=aroma.affymetrix&version=3.0.0&to=aroma.core" data-mini-rdoc="aroma.core::Explorer">Explorer</a>

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

ArrayExplorer function

Methods:
<table><tr><td>
 </td>
<td> <code>addColorMap</code> </td>
</tr><tr><td> -</td>
<td>
 </td>
</tr><tr><td> <code>getColorMaps</code> </td>
<td> -</td>
</tr><tr><td>
 </td>
<td> <code>getDataSet</code> </td>
</tr><tr><td> -</td>
<td>
 </td>
</tr><tr><td> <code>getSetTuple</code> </td>
<td> -</td>
</tr><tr><td>
 </td>
<td> <code>nbrOfChipTypes</code> </td>
</tr><tr><td> -</td>
<td>
 </td>
</tr><tr><td> <code>process</code> </td>
<td> -</td>
</tr><tr><td>
 </td>
<td> <code>setArrays</code> </td>
</tr><tr><td> -</td>
<td>
 </td>
</tr><tr><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, objectSize, print, save, asThis

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

ArrayExplorer: The ArrayExplorer class

Description

Usage

Arguments

Fields and Methods