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Nucleic Acids Research 2005 33(22):e193; doi:10.1093/nar/gni193
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Published online 14 December 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Methods Online

Integrating probe-level expression changes across generations of Affymetrix arrays

Laura L. Elo1,2,*, Leo Lahti2,3, Heli Skottman2,4, Minna Kyläniemi2, Riitta Lahesmaa2 and Tero Aittokallio1,2

1Department of Mathematics, FIN-20014 University of Turku Finland 2Turku Centre for Biotechnology PO Box 123, FIN-20521 Turku, Finland 3Laboratory of Computer and Information Science, Helsinki University of Technology PO Box 5400, FIN-02015 HUT, Finland 4Institute for Regenerative Medicine Regea, University of Tampere and Tampere University Hospital FIN-33520, Tampere, Finland

*To whom correspondence should be addressed. Tel: +358 2 333 8002; Fax: +358 2 333 8000; Email: laliel{at}utu.fi

Received August 16, 2005. Revised October 31, 2005. Accepted November 28, 2005.

There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene expression levels within or between different platforms, we propose a novel meta-analytic method that takes into account the vast amount of available probe-level information to combine the expression changes across different studies. We first show that the comparability of relative expression changes and the consistency of differentially expressed genes between different Affymetrix array generations can be considerably improved by determining the expression changes at the probe-level and by considering the latest information on probe-level sequence matching instead of the probe annotations provided by the manufacturer. With the improved probe-level expression change estimates, data from different generations of Affymetrix arrays can be combined more effectively. This will allow for the full exploitation of existing results when designing and analyzing new experiments.


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[Abstract] [Full Text] [PDF]


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