initialize,ProjectInfo-method

initialize,TreeSet-method

initialize,SchemeTreeSet-method

initialize,ProcesSet-method

initialize,DataTreeSet-method

initialize,ExprTreeSet-method

initialize,CallTreeSet-method

initialize,QualTreeSet-method

initialize,Filter-method

initialize,PreFilter-method

initialize,UniFilter-method

initialize,FilterTreeSet-method

initialize,AnalysisTreeSet-method

initialize-methods

initialize

methods

The package handles pre-processing, normalization, filtering
and analysis of Affymetrix GeneChip expression arrays, including exon
arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST)
and plate arrays on computers with 1 GB RAM only. It imports Affymetrix
.CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA,
MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to
XPS (eXpression Profiling System), which is based on ROOT, an object-oriented
framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite
for the usage of this package, however, no knowledge of ROOT is required.
ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

Christian Stratowa

Processing and Analysis of Affymetrix Oligonucleotide Arrays including
Exon Arrays, Whole Genome Arrays and Plate Arrays

initialize-methods function

<dl>
 Internal method to initialize S4 classes.
</dl> 

Methods

Initialize Classes

initialize-methods: Initialize Classes

Description

Arguments

Methods