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Potential Bias in GO::TermFinder

Journal article published in 2008 by Robert M. Flight ORCID, Peter D. Wentzell
This paper is available in a repository.
This paper is available in a repository.

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Preprint: policy unknown
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Postprint: policy unknown
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Abstract

The increased need for multiple statistical comparisons under conditions of non-independence in bioinformatics applications, such as DNA microarray data analysis, has led to the development of alternatives to the conventional Bonferroni correction for adjusting P-values. The use of the false discovery rate (FDR), in particular, has grown considerably. However, the calculation of the FDR frequently depends on drawing random samples from a population, and inappropriate sampling will result in a bias in the calculated FDR. In this work, we demonstrate a bias due to incorrect random sampling in the widely used GO::Term Finder package. Both T(2) and permutation tests are used to confirm the bias for a test set of data, which leads to an overestimation of the FDR of about 10. A simple fix to the random sampling method is proposed to remove the bias.