Published online 23 January 2006
Methods Online |
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
Institut für Genetik, Universität Köln Zülpicherstrasse 47, 50674 Köln, Germany 1Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien Veterinärplatz 1, 1210 Wien, Austria
*To whom correspondence should be addressed. Tel: +49 221 470 2324; Fax: +49 221 470 5975; Email: harrb{at}uni-koeln.de
Received September 25, 2005. Revised November 9, 2005. Accepted January 3, 2006.
Oligonucleotide microarrays are an informative tool to elucidate gene regulatory networks. In order for gene expression levels to be comparable across microarrays, normalization procedures have to be invoked. A large number of methods have been described to correct for systematic biases in microarray experiments. The performance of these methods has been tested only to a limited extend. Here, we evaluate two different types of microarray analyses: (i) the same gene in replicate samples and (ii) different, but co-expressed genes in the same sample. The reliability of the latter analysis needs to be determined for the analysis of regulatory networks and our report is the first attempt to evaluate for the accuracy of different microarray normalization methods in this respect. Consistent with previous results we observed a large effect of the normalization method on the outcome of the expression analyses. Our analyses indicate that different normalization methods should be performed depending on whether a study is aiming to detect differential gene expression between independent samples or whether co-expressed genes should be identified. We make recommendations about the most appropriate method to use.
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