We are planning an experiment to study the effects of new drugs on animal models of epilepsy. The experiment will be in run in 2 phases.
The hypothesis in Phase 1 is: "Animals receiving Drug X experience a reduction in seizures." Experimental design: One group of control animals and 5 groups of test animals, each receiving a different test drug. Hence, 5 separate comparisons of Test Drug v Control.
The two best drugs from Phase 1 will be taken into Phase 2. In Phase 2, the two test drugs are withdrawn and animals are observed for any persisting benefit.
The hypothesis in Phase 2 is: "Animals that have received Drug X in the past continue to experience enduring benefit." Experimental design: One control group of animals and 2 test groups, each having received a test drug in the past. Hence, 2 separate comparisons of Test Drug vs Control.
Any drug effective in Phase 2 will be taken into human clinical trials. If no drug is effective in Phase 2, then any drug(s) effective in Phase 1 will be taken into human clinical trials. Rationale: any drug which produces enduring benefit even after stopping it would be of greatest interest. However, any drug that is effective while being administered is still of interest. (Additional detail added in response to initial replies.)
How should Bonferroni correction be applied? Separately for each phase , i.e., 0.01 (=0.05/5) for Phase 1 and 0.025 (=0.05/2) for Phase 2? Or 0.007 (=0.05/7) across both phases?