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## 5 GWAS examples 

In this section we demonstrate the suggested methods on two real data examples and on a GWAS simulation. A replicability analysis with FWER control is carried out for the first example, that has only five hypotheses in the follow-up study. A replicability analysis with FDR control is carried out for the second example, that has 126 hypotheses in the follow-up study. Finally, in order to examine the robustness of procedure 3.2 for GWAS type dependency, examples were simulated that retained the dependencies in the data that occur in GWAS. 

Example 1. We reproduce in Table 1, columns 1-4, a subset of the columns of Table 1 of results of Bis et al. (2012). We added in columns 5-7 the Bonferroni- replicability adjusted p -values for c = q$_{1}$/q ∈ { 0 . 2 , 0 . 5 , 0 . 8 } . Procedure 3.1 with parameters ( q$_{1}$, q ) = (0 . 025 , 0 . 05) or ( q$_{1}$, q ) = (0 . 04 , 0 . 05) identified the SNP near MSRB3 as having replicated association with the phenotype. The choice of c should be made prior to analysis, and the choice c = 0 . 8 may be preferred over c ≤ 0 . 5 when it is believed that the power to detect an association in the primary study using a threshold of order 1 / (2 . 5 × 10 $^{6}$) is smaller than the power to detect an association in the follow-up study using a threshold of order 1 / 5. 

