affy—analysis of Affymetrix GeneChip data at the probe level (original) (raw)

Abstract

Motivation: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used.

Results: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.

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Author notes

1Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Building 208, 2800 Lyngby, Denmark, 2Department of Mathematical Sciences, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA, 3Group in Biostatistics, University of California, Berkeley, CA 94720, USA and 4Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe St E3035, Baltimore, MD 21218, USA