Abstract

The simultaneous testing of a large number of hypotheses in a genome scan, using individual thresholds for significance, inherently leads to inflated genome-wide false positive rates. There exist various approaches to approximating the correct genomewide p-values under various assumptions, either by way of asymptotics or simulations. We explore a philosophically different criterion, recently proposed in the literature, which controls the false discovery rate. The test statistics are assumed to arise from a mixture of distributions under the null and non-null hypotheses. We fit the mixture distribution using both a nonparametric approach and commingling analysis, and then apply the local false discovery rate to select cut-off points for regions to be declared interesting. Another criterion, the minimum total error, is also explored. Both criteria seem to be sensible alternatives to controlling the classical type I and type II error rates.

Department(s)

Mathematics

Document Type

Article

DOI

https://doi.org/10.1186/1471-2156-6-s1-s23

Rights Information

© 2005 The author(s). This is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).

Publication Date

2005

Journal Title

In BMC genetics

Share

COinS