False Positive Rates for simulated data for various workflows.

Shown are FPRs under the null hypothesis of no phenotypic effect, estimated by resampling simulated controls. The y-axis’s show box-and-whisker plots of the distribution of the FPR, defined as the fraction of resampled datasets significant at the nominal 5% level in a mixed model. A: FPRs of the test of genotype effect. B: FPRs of the test of genotype-by-sex effect. The labels relate to the workflows as defined in table one where MG indicates the Multi-Group, B2 the TwoBatch, B1 the OneBatch and B3 the ThreeBatch workflows.