Separate analyses of Caucasians and African Americans were conducted to avoid errors due to population stratification. For each DNA microarray (one of two duplicate pools), a “background” value was calculated as the average fluorescence intensity from the 5% of cells with the lowest values; the “background” value was then subtracted from the intensity value of each cell. The background subtracted intensity values were then normalized by dividing by a “ceiling” value, which was the mean intensity of the 5% of cells with the highest values. The normalized A and B probe intensities were averaged from ten “perfect match” intensity values for each A and B probe. The methods are outlined in Johnson, et al. (Johnson et al., 2006). The ratio of averaged and normalized A probe intensity to the sum of averaged and normalized A plus B probe intensity was determined for each variant. The pooled A allele frequency was the average ratio from the duplicate arrays, and this value was used below.
