The exclusion of SNPs strongly associated with any of the batch-variables were based on their minimum P-value across all associations per variable. The cut-off for the wave and Array.Batch was min(P) <2x10−10 and for PreProc. Plate and ArrayPlate.ID min(P) <2x10−12, based on a Bonferroni correction for the number of markers tested and the number of associations done per batch-variable taking into account that batch variables are nested.
