Comparison of Affymetrix GeneChip expression measures.
BACKGROUND
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.


BACKGROUND
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


BACKGROUND
rafa@jhu.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Irizarry
Rafael A
RA
Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA. rafa@jhu.edu
Wu
Zhijin
Z
Jaffee
Harris A
HA
D000465:Algorithms; D019985:Benchmarking; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software