Comparison of Affymetrix GeneChip expression measures

Irizarry, Rafael A.
Wu, Zhijin
Jaffee, Harris A.

¹Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA
²Center for Statistical Sciences, Department of Community Health, Brown University, 167 Angell Street, BOX G-H, Providence, RI 02912, USA

Received on August 25, 2005; revised on and accepted on January 5, 2006; Advance Access publication January 12, 2006

Associate Editor: Chris Stoeckert

Availability: The affycomp package, now version 1.5.2, continues to be available as part of the Bioconductor project (http://www.bioconductor.org). The webtool continues to be available at http://affycomp.biostat.jhsph.edu

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

^*To whom correspondence should be addressed.

Bioinformatics 22(7):p 789-794, April 1, 2006.

Motivation

In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted.

Results

We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently.