Overview of the pair-wise array comparison's performed in this study. Step 1 depicts the construction of three DNA pools. The first two pools (orange and red) are constructed using the same DNA samples and are pool-construction replicates. The third pool (green) is constructed using difference DNA samples. Step 2 indicates allelotyping on Illumina SNP arrays, where the two arrays allelotyping the orange pool are array replicate. Step 3 shows the three types of pair-wise SNP array comparisons that can be made, along with the sources of error that account for differences in allele frequency estimates on the paired arrays. For Type A comparisons, the arrays being compared were used to allelotype the exact same DNA pool; hence, the only source of variation is the array. For Type B comparisons, the arrays paired were used to allelotype independently constructed but identical pools; thus, variation may arise due to the array and the pool-construction process. For Type C comparisons, the arrays paired were used to allelotype completely independent DNA pools, and variation may be due to the array, pool-construction, or binomial sampling (assuming both pools are independent samples from a single population).