TransformReport

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

TransformReport function

<dl> <dt>inSet</dt>
<dd>The input data set as an <code>AffymetrixCelSet</code>.</dd> <dt>outSet</dt>
<dd>The output data set as an <code>AffymetrixCelSet</code>.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Methods: <table class="table">
<tr><td></td><td><code>getCdf</code></td><td>-</td></tr>
<tr><td></td><td><code>getFullName</code></td><td>Gets the full name of the output data set.</td></tr>
<tr><td></td><td><code>getInputDataSet</code></td><td>Gets the source data set.</td></tr>
<tr><td></td><td><code>getName</code></td><td>Gets the name of the output data set.</td></tr>
<tr><td></td><td><code>getOutputDataSet</code></td><td>Gets the transformed data set.</td></tr>
<tr><td></td><td><code>getPath</code></td><td>Gets the path of the output data set.</td></tr>
<tr><td></td><td><code>getTags</code></td><td>Gets the tags of the output data set.</td></tr>
<tr><td></td><td><code>getUnitNamesFile</code></td><td>-</td></tr>
<tr><td></td><td><code>getUnitTypesFile</code></td><td>-</td></tr>
<tr><td></td><td><code>getYY</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>plotXYCurve</code></td><td>-</td></tr>
<tr><td></td><td><code>plotXYCurveLog2</code></td><td>-</td></tr>
<tr><td></td><td><code>seq</code></td><td>-</td></tr>
<tr><td></td><td><code>writeImageCombined</code></td><td>-</td></tr>
<tr><td></td><td><code>writeImages</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 TransformReport 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>TransformReport</code> 
Directly known subclasses: 
 
public static class TransformReport 
extends Object

The TransformReport class — TransformReport

<dl>

 <dt>inSet</dt>
<dd>The input data set as an <code>AffymetrixCelSet</code>.</dd>

 <dt>outSet</dt>
<dd>The output data set as an <code>AffymetrixCelSet</code>.</dd>

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

</dl>

Methods: <table class='table'>
<tr><td></td><td><code>getCdf</code></td><td>-</td></tr>
<tr><td></td><td><code>getFullName</code></td><td>Gets the full name of the output data set.</td></tr>
<tr><td></td><td><code>getInputDataSet</code></td><td>Gets the source data set.</td></tr>
<tr><td></td><td><code>getName</code></td><td>Gets the name of the output data set.</td></tr>
<tr><td></td><td><code>getOutputDataSet</code></td><td>Gets the transformed data set.</td></tr>
<tr><td></td><td><code>getPath</code></td><td>Gets the path of the output data set.</td></tr>
<tr><td></td><td><code>getTags</code></td><td>Gets the tags of the output data set.</td></tr>
<tr><td></td><td><code>getUnitNamesFile</code></td><td>-</td></tr>
<tr><td></td><td><code>getUnitTypesFile</code></td><td>-</td></tr>
<tr><td></td><td><code>getYY</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfArrays</code></td><td>-</td></tr>
<tr><td></td><td><code>plotXYCurve</code></td><td>-</td></tr>
<tr><td></td><td><code>plotXYCurveLog2</code></td><td>-</td></tr>
<tr><td></td><td><code>seq</code></td><td>-</td></tr>
<tr><td></td><td><code>writeImageCombined</code></td><td>-</td></tr>
<tr><td></td><td><code>writeImages</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

	`getCdf`	-
	`getFullName`	Gets the full name of the output data set.
	`getInputDataSet`	Gets the source data set.
	`getName`	Gets the name of the output data set.
	`getOutputDataSet`	Gets the transformed data set.
	`getPath`	Gets the path of the output data set.
	`getTags`	Gets the tags of the output data set.
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`getYY`	-
	`nbrOfArrays`	-
	`plotXYCurve`	-
	`plotXYCurveLog2`	-
	`seq`	-
	`writeImageCombined`	-
	`writeImages`	-

TransformReport: The TransformReport class

Description

Usage

Arguments

Fields and Methods

Author