To overcome the limitations of standard approaches, Storey et al. used a novel statistical approach that exploited what they had the most of—data. They began by determining the single most significant locus for each expression trait. They then moved on to the next most significant locus for that trait, but tested its linkage (that is, its influence on expression) with the assumption that the first locus was also linked. The ability to assign a “probability of linkage” to the first locus greatly simplified the calculations for the subsequent locus, reducing by almost a thousand-fold the number of possibilities that needed to be tested.

As opposed to standard methods, the authors show that their approach is able to assess true