QualityAssessmentModel

A <code><a href="/link/ProbeLevelModel?package=aroma.affymetrix&version=2.11.1" rd-options="" data-mini-rdoc="aroma.affymetrix::ProbeLevelModel">ProbeLevelModel</a></code>.

A <code><a href="/link/character?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::character">character</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of tags.

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

QualityAssessmentModel function

Methods:<tabular>rll</tabular>{
 	<code>getChipEffectSet</code> 	-	<code>getDataSet</code> 	-	<code>getFullName</code> 	-	<code>getName</code> 	-	<code>getPath</code> 	-	<code>getPlm</code> 	-	<code><a href="/link/getResiduals?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetResiduals.QualityAssessmentModel" rd-options="aroma.affymetrix:getResiduals.QualityAssessmentModel" data-mini-rdoc="aroma.affymetrix:getResiduals.QualityAssessmentModel::getResiduals">getResiduals</a></code> 	Calculates the residuals from a probe-level model.	<code>getTags</code> 	-	<code><a href="/link/getWeights?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AgetWeights.QualityAssessmentModel" rd-options="aroma.affymetrix:getWeights.QualityAssessmentModel" data-mini-rdoc="aroma.affymetrix:getWeights.QualityAssessmentModel::getWeights">getWeights</a></code> 	Calculates the weights from the robust fit to a probe-level model.	<code>nbrOfArrays</code> 	-	<code>plotNuse</code> 	-	<code>plotRle</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

QualityAssessmentModel: The QualityAssessmentModel class

Description

Usage

Arguments

Fields and Methods