It turns out that differences in coverage between chips are often not reflected in substantial differences in power and that the use of genotype imputation further reduces these differences. Study power is routinely used throughout science in experimental design and we argue that it should be the primary consideration in designing GWAs. This approach was used in settling several design questions in the Wellcome Trust Case Control Consortium [5]. Our results have been encapsulated in a user-friendly R package that allows the power of different chip and sample size combinations to be assessed given a total budget for the study.
