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- Title
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.
- Authors
Kuo, Winston Patrick; Liu, Fang; Trimarchi, Jeff; Punzo, Claudio; Lombardi, Michael; Sarang, Jasjit; Whipple, Mark E; Maysuria, Malini; Serikawa, Kyle; Lee, Sun Young; McCrann, Donald; Kang, Jason; Shearstone, Jeffrey R; Burke, Jocelyn; Park, Daniel J; Wang, Xiaowei; Rector, Trent L; Ricciardi-Castagnoli, Paola; Perrin, Steven; Choi, Sangdun; Bumgarner, Roger; Kim, Ju Han; Short, Glenn F, 3rd; Freeman, Mason W; Seed, Brian; Jensen, Roderick; Church, George M; Hovig, Eivind; Cepko, Connie L; Park, Peter; Ohno-Machado, Lucila; Jenssen, Tor-Kristian
- Abstract
Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
- Publication
Nature biotechnology, 2006, Vol 24, Issue 7, p832
- ISSN
1087-0156
- Publication type
Journal Article
- DOI
10.1038/nbt1217