ranking differentially expressed genes from affymetrix gene expression data methods with reproducibility, sensitivity, and specificity排名从affymetrix基因表达数据的差异表达基因的方法重现性、灵敏度和特异性.pdfVIP

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ranking differentially expressed genes from affymetrix gene expression data methods with reproducibility, sensitivity, and specificity排名从affymetrix基因表达数据的差异表达基因的方法重现性、灵敏度和特异性.pdf

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ranking differentially expressed genes from affymetrix gene expression data methods with reproducibility, sensitivity, and specificity排名从affymetrix基因表达数据的差异表达基因的方法重现性、灵敏度和特异性

Algorithms for Molecular Biology BioMed Central Research Open Access Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity Koji Kadota*, Yuji Nakai and Kentaro Shimizu Address: Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan Email: Koji Kadota* - kadota@bi.a.u-tokyo.ac.jp; Yuji Nakai - aynakai@mail.ecc.u-tokyo.ac.jp; Kentaro Shimizu - shimizu@bi.a.u-tokyo.ac.jp * Corresponding author Published: 22 April 2009 Received: 14 November 2008 Accepted: 22 April 2009 Algorithms for Molecular Biology 2009, 4:7 doi:10.1186/1748-7188-4-7 This article is available from: /content/4/1/7 © 2009 Kadota 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: To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression- level measurements and a way of ranking genes to obtain the most plausible candidates. We recently recommended suitable combinations of a preprocessing algorithm and gene ranking method that can be used to identify DEGs with a higher level of sensitivity and specificity. However, in addition to these recommendations, resear