An R Package for Analyses of Affymetrix Oligonucleotide Arrays

We describe an extensible, interactive environment for data analysis and exploration of Affymetrix oligonucleotide array probe-level data. The software utilities provided with the Affymetrix analysis suite summarize the probe set intensities and makes available only one expression measure for each gene. We have developed this package because much can be learned from studying the individual probe intensities or, as we call them, the probe-level data. We provide some examples demonstrating that having access to and methods for probelevel data results in improvements to quality control assessments, normalization, and expression measures. The software is implemented as an add-on package, conveniently named affy, to the freely available and widely used statistical language/software R (Ihaka and Gentleman, 1996). The development of this software as an add-on to R allows us to take advantage of the basic mathematical and statistical functions and powerful graphics capabilities that are provided with R. Our package is distributed as open source code for Linux, Unix, and Microsoft Windows. It is is released under the GNU General Public License. It is part of the Bioconductor project and can be obtained from http://www.bioconductor.org.