TransformReport

The input data set as an <code><a href="/link/AffymetrixCelSet?package=aroma.affymetrix&version=2.11.1" rd-options="" data-mini-rdoc="aroma.affymetrix::AffymetrixCelSet">AffymetrixCelSet</a></code>.

inSet

The output data set as an <code><a href="/link/AffymetrixCelSet?package=aroma.affymetrix&version=2.11.1" rd-options="" data-mini-rdoc="aroma.affymetrix::AffymetrixCelSet">AffymetrixCelSet</a></code>.

outSet

Package: aroma.affymetrix Class TransformReport<code><a href="/link/Object?package=aroma.affymetrix&version=2.11.1&to=R.oo" rd-options="R.oo" data-mini-rdoc="R.oo::Object">Object</a></code><code>~~|</code><code>~~+--</code><code>TransformReport</code>Directly known subclasses:public static class TransformReportextends <a href="/link/Object?package=aroma.affymetrix&version=2.11.1&to=R.oo" rd-options="R.oo" data-mini-rdoc="R.oo::Object">Object</a>

classes

This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.  These are designed to be memory efficient but still being fast.  The idea is to keep all data on file and only read data into memory when needed.  Clever caching mechanisms are used to minimize the overhead of data IO.  All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory.  With this design it is only the disk space that limits the number of arrays that can be analyzed.

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

TransformReport function

Methods:<tabular>rll</tabular>{
 	<code>getCdf</code> 	-	<code><a href="/link/getFullName?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetFullName.TransformReport" rd-options="aroma.affymetrix:getFullName.TransformReport" data-mini-rdoc="aroma.affymetrix:getFullName.TransformReport::getFullName">getFullName</a></code> 	Gets the full name of the output data set.	<code><a href="/link/getInputDataSet?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetInputDataSet.TransformReport" rd-options="aroma.affymetrix:getInputDataSet.TransformReport" data-mini-rdoc="aroma.affymetrix:getInputDataSet.TransformReport::getInputDataSet">getInputDataSet</a></code> 	Gets the source data set.	<code><a href="/link/getName?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetName.TransformReport" rd-options="aroma.affymetrix:getName.TransformReport" data-mini-rdoc="aroma.affymetrix:getName.TransformReport::getName">getName</a></code> 	Gets the name of the output data set.	<code><a href="/link/getOutputDataSet?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetOutputDataSet.TransformReport" rd-options="aroma.affymetrix:getOutputDataSet.TransformReport" data-mini-rdoc="aroma.affymetrix:getOutputDataSet.TransformReport::getOutputDataSet">getOutputDataSet</a></code> 	Gets the transformed data set.	<code><a href="/link/getPath?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetPath.TransformReport" rd-options="aroma.affymetrix:getPath.TransformReport" data-mini-rdoc="aroma.affymetrix:getPath.TransformReport::getPath">getPath</a></code> 	Gets the path of the output data set.	<code><a href="/link/getTags?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetTags.TransformReport" rd-options="aroma.affymetrix:getTags.TransformReport" data-mini-rdoc="aroma.affymetrix:getTags.TransformReport::getTags">getTags</a></code> 	Gets the tags of the output data set.	<code>getUnitNamesFile</code> 	-	<code>getUnitTypesFile</code> 	-	<code>getYY</code> 	-	<code>nbrOfArrays</code> 	-	<code>plotXYCurve</code> 	-	<code>plotXYCurveLog2</code> 	-	<code>seq</code> 	-	<code>writeImageCombined</code> 	-	<code>writeImages</code> 	-}
 Methods inherited from Object:$, $&lt;-, [[, [[&lt;-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

TransformReport: The TransformReport class

Description

Usage

Arguments

Fields and Methods