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Bioinformatics Advance Access published online on September 24, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm448
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The High-level Similarity of Some Disparate Gene Expression Measures

Nandini Raghavan 1, An M.I.M. De Bondt 2, Willem Talloen 3, Dieder Moechars 2, Hinrich W.H. Göhlmann 2 and Dhammika Amaratunga *,1

1Nonclinical Biostatistics, Johnson & Johnson Pharmaceutical Research & Development LLC, Raritan, NJ 08869, USA.
2Functional genomics, Johnson & Johnson Pharmaceutical Research & Development. A Division of Janssen Pharmaceutica, B-2340, Beerse, Belgium.
3Nonclinical Biostatistics, Johnson & Johnson Pharmaceutical Research & Development, A Division of Janssen Pharmaceutica, B-2340, Beerse, Belgium.

*To whom correspondence should be addressed. Dr. Dhammika Amaratunga, E-mail: damaratu{at}prdus.jnj.com


  Abstract

Probe level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures. Disturbingly, the different approaches not only generate quite different measures but they could also yield very different analysis results. Here we explore the question of how much the analysis results really do differ, first at the gene level, then at the biological process level. We demonstrate that, even though the gene level results may not necessarily match each other particularly well, as long as there is reasonably strong differentiation between the groups in the data, the various gene expression measures do in fact produce results that are similar to one another at the biological process level. Not only that, the results are biologically relevant. As the extent of differentiation drops, the degree of concurrence weakens, although the biological relevance of findings at the biological process level may yet remain.

Abbreviation: GEM (gene expression measure).

Associate Editor: Prof. Martin Bishop

Received on May 11, 2007; revised on August 24, 2007; accepted on August 25, 2007

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