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associations is at most the set of SNPs that are discovered by the BH procedure (as discussed in Section 3). Table 2 presents the average number of replicated findings, as well as the average false discovery proportion (FDP) for the methods compared. The standard error (SE) is presented in parentheses. From rows 1 and 2 we see that if there is no division into primary and follow-up studies, then the symmetric Procedure 4.1 discovers more SNPs with replicated associations than the BH procedure on maximum p -values, while maintaining a low FDP. From rows 3-5, and 6-8, we see that the choice of which study was the primary study had a large effect on the average number of discoveries, and the choice of q$_{1}$ mattered little. 

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From the last column in Table 2 we see that the average FDP was far below 0.05, suggesting that the procedures are conservative. This conservatism can be alleviated if the following oracle information were known: the fraction of SNPs with no association with the phenotype in both studies, f$_{00}$ , and with association with the phenotype only in the follow-up study, f$_{01}$ . Then it was possible to perform Procedure 4.1 at level ( w$_{1}$, q $^{′}$, 2 q $^{′}$), where q ′ is the solution to f$_{00}$ ( q $^{′}$) $^{2}$+( f$_{01}$ +1) q ′ = q for w$_{1}$ ∈ { 0 , 1 } , and the solution to f$_{00}$ (0 . 5 q $^{′}$) 2 + ( f$_{01}$ + 1)0 . 5 q ′ = 0 . 5 q for w$_{1}$ = 0 . 5, with the same guarantee 

