Table 3.

Probability of declaring equivalence (pr(Rej) for the normal test, $p{r}_B(Rej)$ for the bootstrap test) when the simulated dissimilarity is equal to the equivalence limit, $d_S=d_0$.

nSim	$d_S$	$d_0$	$p_{11}$	$p_{01}$	$p_{10}$	pr(Rej)	$p{r}_B(Rej)$	$E(\nu )$
100000	0.2857	0.2857	0.01250	0.005	0.005	0.0590	0.0498	225.00
100000	0.2857	0.2857	0.01875	0.005	0.010	0.0570	0.0499	337.50
100000	0.2857	0.2857	0.02500	0.010	0.010	0.0560	0.0502	450.00
100000	0.2857	0.2857	0.06875	0.005	0.050	0.0534	0.0485	1237.50
100000	0.2857	0.2857	0.07500	0.010	0.050	0.0532	0.0500	1350.00
100000	0.2857	0.2857	0.12500	0.050	0.050	0.0527	0.0503	2250.00
100000	0.2857	0.2857	0.13125	0.005	0.100	0.0524	0.0499	2362.50
100000	0.2857	0.2857	0.13750	0.010	0.100	0.0524	0.0502	2475.00
100000	0.2857	0.2857	0.18750	0.050	0.100	0.0522	0.0503	3375.00
100000	0.2857	0.2857	0.25000	0.100	0.100	0.0519	0.0502	4500.00
100000	0.2857	0.2857	0.25625	0.005	0.200	0.0518	0.0501	461.25
100000	0.2857	0.2857	0.26250	0.010	0.200	0.0516	0.0501	4725.00
100000	0.2857	0.2857	0.31250	0.050	0.200	0.0513	0.0499	5625.00
100000	0.2857	0.2857	0.37500	0.100	0.200	0.0513	0.0499	6750.00
100000	0.2857	0.2857	0.50000	0.200	0.200	0.0512	0.0501	9000.00

$n=10000$ stands for the total number of GO terms, with $p_{\mathit{ij}}$ probabilities of enrichment. $E(\nu )$ is the expected total number of enriched terms. nsim corresponds to the number of effective simulation replicates to obtain $p{r}_B(Rej)$ ($nsim\times B$ test computations, $B=10000$; pr(Rej) was based on ${10}^6$ simulation replicates)