Empirical estimates of Bonferroni corrections for use in chromosome mapping studies with the BXD recombinant inbred...

Most chromosome mapping efforts with the BXD recombinant inbred (RI) strains involve comparisons between a trait of interest and each of a large number of marker loci for evidence of linkage. Such multiple tests or comparisons greatly increase the Type I error rate compared to the single-test situation. Perhaps the most direct way to obtain multiple-test error rates is to employ a Bonferroni correction, where the single-test alpha is multiplied by the number of independent (nonredundant) comparisons (k) to yield a multiple-test alpha that protects against even one fortuitous association with any of the markers. Several empirical estimates of k are discussed for the published BXD marker set of 142 mapped loci and the newer unpublished marker set (October 1991) comprised of 352 marker loci. Reasonable estimates of k appear to be roughly 40 and 65 for these two marker sets, respectively.