As has been observed in SNP genotyping20, results of association analyses using Canary CNP genotypes can be sensitive to differential bias that can arise when data from individual plates or batches are incorrectly clustered. It is prudent to search for any individual plates or batches for which the Canary clustering may be incorrect; this can be accomplished by visual inspection of the underlying intensity data, or by automated identification of individual plates for which the frequency of the observed genotype classes is statistically unusual given the distribution on the other plates.
