False Positive Rates for other institutes for various workflows.

Shown are FPRs under the null hypothesis of no phenotypic effect, estimated by resampling controls from two independent institutes for various workflows. 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, B: Resampling results using data from the German Mouse Clinic, where A is the FPR for genotype effect and B is the FPR for genotype-by-sex effect. C, D: Results using control data from Institut Clinique de la Souris, where C is the FPRs for the genotype effect and D the FPRs for the genotype-by-sex effect. The labels relate to the workflows as defined in table one where MG indicates the Multi-Group, R the Random, B2 the TwoBatch, B1 the OneBatch and B3 the ThreeBatch workflows.