False Positive Rates for resampling control data for various workflows.

Shown are FPRs under the null hypothesis of no phenotypic effect, estimated by resampling controls for various workflows, for 70 traits from five assays from the WTSI Mouse Genetics Project (MGP) Select Pipeline. The y-axis shows 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: FPR of the test of genotype effect. B: FPR of the test of sex by genotype interaction. 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.