is to be performed (e.g. using the --assoc option in PLINK), and both the average p-value and the number of results significant at a certain threshold (e.g. p<1×10−4) can be recorded. SNPs with low minor allele frequency (i.e. <5%) should be removed before this analysis is performed to improve the stability of test statistics. This procedure should be repeated for each plate or batch in the study. If any single plate has many more or many fewer significant results, or has an average p-value that deviates from 0.5 (under the null the average p-value will be 0.5 over many tests), then this batch should be further investigated for genotyping or composition problems. If batch effects are present, methods similar to those used for population stratification (e.g. genomic control) may be used to mitigate the confounding effects.
