The multiplicity problem in linkage analysis of gene expression data – the power of differentiating cis- and trans-acting regulators

In this report, we focused on the multiplicity issue in Problem 1 of Genetic Analysis Workshop 15. We investigated and compared the performance of the stratified false-discovery rate control method with the traditional aggregated approach, in an application to genome-wide linkage analyses of single-nucleotide polymorphism-to-gene expression data. We showed the importance of utilizing the available map information and demonstrated the power gained by conducting false-discovery rate control separately for cis and trans regulators under three different frameworks: fixed rejection region, fixed false-discovery rate, and fixed number of rejections.