affy—analysis of <i>Affymetrix GeneChip</i> data at the probe level

TLDR

The processing of Affymetrix GeneChip data has recently attracted attention, and alternative methods to the original procedure have been proposed and widely adopted. The paper presents the main classes and functions of the affy package and demonstrates their use for probe‑level data processing. The affy R package, now in its second release, offers extensive flexibility for analyzing Affymetrix oligonucleotide arrays, enabling users to access and manipulate probe‑intensity data through a suite of functions and classes. The study demonstrates that probe‑level analysis is crucial when using the Affymetrix GeneChip platform.

Abstract

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.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.