Table 2.

Probability of declaring equivalence (pr(Rej) normal test, $p{r}_B(Rej)$ bootstrap test) for a simulated dissimilarity equal to the equivalence limit, $d_S=d_0$. $n=1000$ stands for the total number of GO terms, with $p_{\mathit{ij}}$ probabilities of enrichment.

nSim	${\mathbf{d}}_{\mathbf{S}}$	${\mathbf{d}}_{\mathbf{0}}$	${\mathbf{p}}_{\mathbf{11}}$	${\mathbf{p}}_{\mathbf{01}}$	${\mathbf{p}}_{\mathbf{10}}$	pr(Rej)	${\mathbf{pr}}_{\mathbf{B}}(\mathbf{Rej})$	$\mathbf{E}(\nu )$
99433	0.2857	0.2857	0.01250	0.005	0.005	0.0807	0.0251	22.50
99994	0.2857	0.2857	0.01875	0.005	0.010	0.0741	0.0371	33.75
100000	0.2857	0.2857	0.02500	0.010	0.010	0.0706	0.0417	45.00
100000	0.2857	0.2857	0.06875	0.005	0.050	0.0617	0.0485	123.75
100000	0.2857	0.2857	0.07500	0.010	0.050	0.0614	0.0483	135.00
100000	0.2857	0.2857	0.12500	0.050	0.050	0.0591	0.0500	225.00
100000	0.2857	0.2857	0.13125	0.005	0.100	0.0584	0.0493	236.25
100000	0.2857	0.2857	0.13750	0.010	0.100	0.0583	0.0496	247.50
100000	0.2857	0.2857	0.18750	0.050	0.100	0.0568	0.0499	337.50
100000	0.2857	0.2857	0.25000	0.100	0.100	0.0558	0.0497	450.00
100000	0.2857	0.2857	0.25625	0.005	0.200	0.0558	0.0498	461.25
100000	0.2857	0.2857	0.26250	0.010	0.200	0.0559	0.0497	472.50
100000	0.2857	0.2857	0.31250	0.050	0.200	0.0548	0.0494	562.50
100000	0.2857	0.2857	0.37500	0.100	0.200	0.0541	0.0490	675.00
100000	0.2857	0.2857	0.50000	0.200	0.200	0.0538	0.0495	900.00

$E(\nu )$ is the expected total number of enriched terms. nsim corresponds to the number of effective simulation replicates (over an initial number of ${10}^5$) to obtain $p{r}_B(Rej)$ ($nsim\times B$ test computations, $B=10000$; pr(Rej) was based on an initial number of ${10}^6$ simulation replicates). In some scenarios with low $p_{\mathit{ij}}$, the generated tables contained zeros making impossible the Sorensen–Dice computations, so the effective number of simulation replicates was lower than what was initially planned