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Physiol. Genomics 16: 361-370, 2004. First published November 25, 2003; doi:10.1152/physiolgenomics.00080.2003
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Received 9 May 2003; accepted in final form 17 November 2003.
Physiological Genomics 16:361-370 (2004)
1094-8341/04 $5.00 © 2004 American Physiological Society

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A comparison of oligonucleotide and cDNA-based microarray systems

Nancy Mah 1, Anders Thelin 2, Tim Lu 1, Susanna Nikolaus 1, Tanja Kühbacher 1, Yesim Gurbuz 3, Holger Eickhoff 4, Günther Klöppel 3, Hans Lehrach 4, Björn Mellgård 2, Christine M. Costello 1,* and Stefan Schreiber 1,*

1 First Department of Medicine, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany
2 AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
3 Department of Pathology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany
4 Max-Planck Institute for Molecular Genetics, D-14195 Berlin, Germany

Large-scale public data mining will become more common as public release of microarray data sets becomes a corequisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely, an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in "present" or "absent" calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors, or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms.

noncommercial clone-based microarray system; commercial oligonucleotide-based microarray system; expression screening platform; cross-platform screening




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