Table 1 compares the allele calls for the two platforms for the 94 SNPs using all of the Collaborative Study on the Genetics of Alcoholism (COGA) data. The numbers in parentheses are the counts prior to data cleaning. As expected, the number of no-calls increased in the clean data as a result of removing Mendelian incompatibilities. For the 116,457 occurrences in which a genotype call could be made with both platforms, a total of 180 (0.15%) are discrepant. None of these discrepancies gives rise to a Mendelian non-inheritance, in part because of the data cleaning process that selectively removed an "offending" genotype.
