the same procedure that had been followed for the actual data was run. The number of trials for which the results from the randomly-selected set of SNPs matched or exceeded the results actually observed from the SNPs identified in the current study was tabulated. Empirical p values were calculated by dividing the number of trials for which the observed results were matched or exceeded by the total number of Monte Carlo simulation trials performed. Since this method examines the properties of the SNPs in the current dataset, assuming independence of their allele frequencies, it should be relatively robust despite the uneven distribution of Affymetrix SNP markers across the genome.
