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Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.doc

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Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data

BMC Bioinformatics BioMedCentral Research article Open Access Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data Kerby Shedden*1, Wei Chen2, Rork Kuick3, Debashis Ghosh2, James Macdonald4, Kathleen R Cho5, Thomas J Giordano5, Stephen B Gruber6, Eric R Fearon6, Jeremy MG Taylor2 and Samir Hanash3 Address: 1Department of Statistics, University of Michigan, Ann Arbor, Michigan, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA, 3Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA, 4Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA, 5Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA and 6Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Email: Kerby Shedden* - kshedden@; Wei Chen - lisachen@; Rork Kuick - rork@; Debashis Ghosh - ghoshd@; James Macdonald - jmacdon@; Kathleen R Cho - kathcho@; Thomas J Giordano - giordano@; Stephen B Gruber - sgruber@; Eric R Fearon - fearon@; Jeremy MG Taylor - jmgt@; Samir Hanash - shanash@ * Corresponding author Published: 10 February 2005 Received: 26 October 2004 Accepted: 10 February 2005 BMC Bioinformatics 2005, 6:26 doi:10.1186/1471-2105-6-26 This article is available from: /1471-2105/6/26 ? 2005 Shedden et al; 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: A critical step in processing oligonucleotide microarray data is combining the information in multiple probes to produce a single number that best captures the expression level of a RNA transcript. Several systematic studies comparing multiple methods for array processing have used t