A benchmark for Affymetrix GeneChip expression measures

Authors:
Leslie M. Cope;Rafael A. Irizarry;Harris A. Jaffee;Zhijin Wu;Terence P. Speed
Affiliations:
Department of Mathematical Sciences, Johns Hopkins University, 104 Whitehead Hall, 3400 North Charles Street, Baltimore, MD 21218, USA,;Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA;Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA;Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA;Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, CA 94720, USA
Venue:
Bioinformatics
Year:
2004

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Abstract

Motivation: The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create probeset summaries with specific characteristics. There are now several methods available for summarizing probe level data from the popular Affymetrix GeneChips, but it is difficult to identify the best method for a given inquiry. Results: We have developed a graphical tool to evaluate summaries of Affymetrix probe level data. Plots and summary statistics offer a picture of how an expression measure performs in several important areas. This picture facilitates the comparison of competing expression measures and the selection of methods suitable for a specific investigation. The key is a benchmark data set consisting of a dilution study and a spike-in study. Because the truth is known for these data, we can identify statistical features of the data for which the expected outcome is known in advance. Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data. Availability: In conjunction with the release of a graphics toolbox as part of the Bioconductor project (http://www.bioconductor.org), a webtool is available at http://affycomp.biostat.jhsph.edu. Supplemental material is available at http://www.biostat.jhsph.edu/~ririzarr/papers/suppaffycomp.pdf