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Bioinformatics 2007 23(13):i313-i318; doi:10.1093/bioinformatics/btm182
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Biases induced by pooling samples in microarray experiments

Tristan Mary-Huard 1,*, Jean-Jacques Daudin 1, Michela Baccini 2,3, Annibale Biggeri 2,3 and Avner Bar-Hen 1

1UMR AgroParisTech/INRA MIA 518, 16 rue Claude Bernard 75231 Paris Cedex 5 (France) and 2Department of Statistics ‘G. Parenti’, viale Morgagni 59, 50100 and 3 CSPO Biostatistics Unit, via San Salvi, Florence, Italy

*To whom correspondence should be addressed.


  Abstract

Motivation: If there is insufficient RNA from the tissues under investigation from one organism, then it is common practice to pool RNA. An important question is to determine whether pooling introduces biases, which can lead to inaccurate results. In this article, we describe two biases related to pooling, from a theoretical as well as a practical point of view.

Results: We model and quantify the respective parts of the pooling bias due to the log transform as well as the bias due to biological averaging of the samples. We also evaluate the impact of the bias on the statistical differential analysis of Affymetrix data.

Contact: maryhuar{at}inapg.fr


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