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PubMed · 15846361

Multiple-laboratory comparison of microarray platforms.

Rafael A Irizarry·Daniel Warren·Forrest Spencer·Irene F Kim·Shyam Biswal·Bryan C Frank·Edward Gabrielson·Joe G N Garcia·Joel Geoghegan·Gregory Germino·Constance Griffin·Sara C Hilmer·Eric Hoffman·Anne E Jedlicka·Ernest Kawasaki·Francisco Martínez-Murillo·Laura Morsberger·Hannah Lee·David Petersen·John Quackenbush·Alan Scott·Michael Wilson·Yanqin Yang·Shui Qing Ye·Wayne Yu
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Abstract

Microarray technology is a powerful tool for measuring RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross-platform meta-analysis studies rapidly increases, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we noticed that none of the previously published papers consider differences between labs. For this study, a consortium of ten laboratories from the Washington, DC-Baltimore, USA, area was formed to compare data obtained from three widely used platforms using identical RNA samples. We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well.

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BaltimoreDistrict of ColumbiaGene Expression ProfilingHumansLaboratoriesOligonucleotide Array Sequence AnalysisReproducibility of ResultsComparative StudyJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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Rafael A Irizarry, Daniel Warren, Forrest Spencer, Irene F Kim, Shyam Biswal, Bryan C Frank, Edward Gabrielson, Joe G N Garcia, Joel Geoghegan, Gregory Germino, Constance Griffin, Sara C Hilmer, Eric Hoffman, Anne E Jedlicka, Ernest Kawasaki, Francisco Martínez-Murillo, Laura Morsberger, Hannah Lee, David Petersen, John Quackenbush, Alan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye, Wayne Yu. 2005-04-21. Multiple-laboratory comparison of microarray platforms.. https://doi.org/10.1038/nmeth756

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