a comparative review of estimates of the proportion unchanged genes and the false discovery rate比较评估估计比例不变的基因和错误发现率.pdfVIP

BMC Bioinformatics BioMed Central Methodology article Open Access A comparative review of estimates of the proportion unchanged genes and the false discovery rate Per Broberg* Address: Biological Sciences, AstraZeneca RD Lund, S-221 87 Lund, Sweden Email: Per Broberg* - per.broberg@ * Corresponding author Published: 08 August 2005 Received: 22 December 2004 Accepted: 08 August 2005 BMC Bioinformatics 2005, 6:199 doi:10.1186/1471-2105-6-199 This article is available from: /1471-2105/6/199 © 2005 Broberg; 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: In the analysis of microarray data one generally produces a vector of p-values that for each gene give the likelihood of obtaining equally strong evidence of change by pure chance. The distribution of these p-values is a mixture of two components corresponding to the changed genes and the unchanged ones. The focus of this article is how to estimate the proportion unchanged and the false discovery rate (FDR) and how to make inferences based on these concepts. Six published methods for estimating the proportion unchanged genes are reviewed, two alternatives are presented, and all are tested on both simulated and