Chunk #14 — 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
list that corresponded to these randomly-assigned numbers were then queried for the extent to which their results equaled or exceeded the results obtained for the actual dataset. In 10,000 such trials for each sample, we compared results concerning the extent of chromosomal clustering from these sets of pseudopositive SNPs to those for the true positive SNPs. These empirical Monte Carlo p values thus addressed the null hypothesis that the true positive SNPs from each single sample were randomly arrayed on the chromosomes. Of course, the clustering of SNPs that provided nominally-significant case vs control differences in each individual sample did not allow us to discern whether the haplotypes identified in such a manner were related to a) phenotypic differences or to b) stochastic differences in haplotype frequencies between case and control samples.
