Chunk #15 — Materials and Methods — Subjects, genotyping and assignment of nominal significance of dependent vs control allele frequencies in each sample — 4) Monte Carlo methods for assignment of levels of significance to: a) the extent of clustering in each sample and b) the degree to which clustered nominally-positive SNPs from multiple independent samples identify the same chromosomal regions
Monte Carlo methods were also used to assign empirical statistical probabilities to a second null hypotheses: that the same chromosomal regions were identified by the clustered, nominally positive SNPs in independent samples with the frequencies expected by chance. In 10,000 trials from pairs of independent samples, we compared the extent of overlap between the chromosomal regions identified by the clustered, nominally-positive SNPs in each sample. The Monte Carlo p values that derive from these trials thus addressed the second null hypothesis that the chromosomal regions identified by clusters of nominally positive SNPs in each of multiple samples were identified only on stochastic bases that were unrelated to phenotype.
