Allele frequencies for each SNP in each DNA pool were assessed based on hybridization to the 12 "perfect match" cells on each of four arrays from replicate experiments, as described [31,55]. In brief, each cell's value was analyzed by subtracting background fluorescence intensities and normalizing background-subtracted values to the values for the highest intensities on each array. We averaged the data from the 12 perfect match cells for A and B alleles for each SNP. To facilitate comparison of data from multiple arrays, we derived the arctangent of the ratio between hybridization intensities for A and B alleles for each array. We then averaged these arctan A/B values for the four replicate arrays that assessed genotype frequencies for each pool. We calculated the mean arctan A/B ratios for nicotine dependent vs control individuals (and for quitters vs nonquitters). We divided the mean arctan A/B ratio for abusers (or quitters) by the mean arctan A/B ratio for controls (or nonquitters) to form abuser/control (or quitter/nonquitter) ratios. We generated a "t" statistic for the differences between abusers and controls or quitters and
