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Nucleic Acids Res. 2003 Feb 15;31(4):e15.

Summaries of Affymetrix GeneChip probe level data.

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP.

Source

Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA. rafa@jhu.edu

Abstract

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.

PMID:: 12582260; [PubMed - indexed for MEDLINE]
PMCID:: PMC150247

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Research Support, U.S. Gov't, P.H.S.

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U01 HL66583/HL/NHLBI NIH HHS/United States

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