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Nucleic Acids Research Advance Access originally published online on August 31, 2009
Nucleic Acids Research 2009 37(19):6323-6339; doi:10.1093/nar/gkp706
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Nucleic Acids Research, 2009, Vol. 37, No. 19 6323-6339
© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions

Igor Dozmorov1,* and Ivan Lefkovits2

1Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA and 2Department of Biomedicine, University Clinics Basel, Vesalianum, Vesalgasse 1, CH-4051 Basel, Switzerland

*To whom correspondence should be addressed. Tel: +1 405 271 7052; Fax: +1 405 271 4002; Email: igor-dozmorov{at}omrf.org

Received February 25, 2009. Revised August 7, 2009. Accepted August 10, 2009.

Genome-scale microarray experiments for comparative analysis of gene expressions produce massive amounts of information. Traditional statistical approaches fail to achieve the required accuracy in sensitivity and specificity of the analysis. Since the problem can be resolved neither by increasing the number of replicates nor by manipulating thresholds, one needs a novel approach to the analysis. This article describes methods to improve the power of microarray analyses by defining internal standards to characterize features of the biological system being studied and the technological processes underlying the microarray experiments. Applying these methods, internal standards are identified and then the obtained parameters are used to define (i) genes that are distinct in their expression from background; (ii) genes that are differentially expressed; and finally (iii) genes that have similar dynamical behavior.


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