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Bioinformatics Advance Access originally published online on January 12, 2006
Bioinformatics 2006 22(7):789-794; doi:10.1093/bioinformatics/btk046
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparison of Affymetrix GeneChip expression measures

Rafael A. Irizarry 1,*, Zhijin Wu 2 and Harris A. Jaffee 1

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

*To whom correspondence should be addressed.

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.

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: rafa{at}jhu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on August 25, 2005; revised on January 5, 2006; accepted on January 5, 2006

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