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.

Keywords

BiologyGene chip analysisDNA microarrayComputational biologySet (abstract data type)Gene expression profilingMicroarray databasesMicroarrayData setGene expressionMicroarray analysis techniquesSuiteGeneticsGeneData miningBioinformaticsComputer scienceArtificial intelligence

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2003 Nucleic Acids Research 486 citations

Publication Info

Year
2003
Type
article
Volume
31
Issue
4
Pages
15e-15
Citations
4931
Access
Closed

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Rafael A. Irizarry, Benjamin M. Bolstad, François Collin et al. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research , 31 (4) , 15e-15. https://doi.org/10.1093/nar/gng015

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DOI
10.1093/nar/gng015