Nucleic Acids Research, 2003, Vol. 31, No. 4 e15
© 2003 Oxford University Press
Summaries of Affymetrix GeneChip probe level data
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA, 1 Biostatistics Group, University of California, Berkeley, CA, USA, 2 Gene Logic Inc., Berkeley, CA, USA, 3 Mathematical Sciences Department, Johns Hopkins University, Baltimore, MD, USA, 4 Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia and 5 Department of Statistics, University of California, Berkeley, CA, USA
*To whom correspondence should be addressed. Tel: +1 410 614 5157; Fax: +1 410 955 0958; Email: rafa{at}jhu.edu
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11–20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.
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