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Open Access Methodology article

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures

Xin Lu12* and David L Perkins23

Author Affiliations

1 Department of Family and Preventive Medicine, UC San Diego, La Jolla, CA, 92093, USA

2 Departments of Medicine, UC San Diego, La Jolla, CA, 92093, USA

3 Departments of Surgery, UC San Diego, La Jolla, CA, 92093, USA

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BMC Bioinformatics 2007, 8:157  doi:10.1186/1471-2105-8-157

Published: 18 May 2007



When conducting multiple hypothesis tests, it is important to control the number of false positives, or the False Discovery Rate (FDR). However, there is a tradeoff between controlling FDR and maximizing power. Several methods have been proposed, such as the q-value method, to estimate the proportion of true null hypothesis among the tested hypotheses, and use this estimation in the control of FDR. These methods usually depend on the assumption that the test statistics are independent (or only weakly correlated). However, many types of data, for example microarray data, often contain large scale correlation structures. Our objective was to develop methods to control the FDR while maintaining a greater level of power in highly correlated datasets by improving the estimation of the proportion of null hypotheses.


We showed that when strong correlation exists among the data, which is common in microarray datasets, the estimation of the proportion of null hypotheses could be highly variable resulting in a high level of variation in the FDR. Therefore, we developed a re-sampling strategy to reduce the variation by breaking the correlations between gene expression values, then using a conservative strategy of selecting the upper quartile of the re-sampling estimations to obtain a strong control of FDR.


With simulation studies and perturbations on actual microarray datasets, our method, compared to competing methods such as q-value, generated slightly biased estimates on the proportion of null hypotheses but with lower mean square errors. When selecting genes with controlling the same FDR level, our methods have on average a significantly lower false discovery rate in exchange for a minor reduction in the power.