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 QuackenbushAlan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye, Wayne Yu

Research output: Contribution to journalArticle

676 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)345-349
Number of pages5
JournalNature Methods
Volume2
Issue number5
DOIs
StatePublished - May 1 2005
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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    Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S. C., Hoffman, E., Jedlicka, A. E., Kawasaki, E., Martínez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., ... Yu, W. (2005). Multiple-laboratory comparison of microarray platforms. Nature Methods, 2(5), 345-349. https://doi.org/10.1038/nmeth756