Combining Affymetrix microarray results.docVIP

BMC Bioinformatics BioMedCentral Methodology article Open Access Combining Affymetrix microarray results John R Stevens1 and RW Doerge*1,2 Address: 1Department of Statistics, Purdue University, 150 N. University Street, West Lafayette, Indiana 47907-2067, USA and 2Department of Agronomy, Purdue University, Lilly Hall of Sciences, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA Email: John R Stevens - jrsteven@; RW Doerge* - doerge@ * Corresponding author Published: 17 March 2005 Received: 28 October 2004 Accepted: 17 March 2005 BMC Bioinformatics 2005, 6:57 doi:10.1186/1471-2105-6-57 This article is available from: /1471-2105/6/57 ? 2005 Stevens and Doerge; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: As the use of microarray technology becomes more prevalent it is not unusual to find several laboratories employing the same microarray technology to identify genes related to the same condition in the same species. Although the experimental specifics are similar, typically a different list of statistically significant genes result from each data analysis. Results: We propose a statistically-based meta-analytic approach to microarray analysis for the purpose of systematically combining results from the different laboratories. This approach provides a more precise view of genes that are significantly related to the condition of interest while simultaneously allowing for differences between laboratories. Of particular interest is the widely used Affymetrix oligonucleotide array, the results of which are naturally suited to a meta-analysis. A simulation model based on the Affymetrix platform is developed to examine the adaptive nature of the meta-analytic