The no-call rate is higher for the Affymetrix platform than for the Illumina platform. In the cleaned data for these 94 SNPs, the difference in the no-call rate is approximately 8.6-fold. There is, however, an interesting pattern in the distribution of no-calls. The Affymetrix no-call rate is 3.79% for genotypes that Illumina calls as homozygous and 6.53% for genotypes that Illumina calls heterozygous. The difference in call rates conditioned on Illumina's genotypes is highly significant (p < 0.0001). This patterning is not present for Illumina no-calls.
