Table 4.

Sensitivity analysis results for the two-study and five-study simulation data. Sensitivity analysis results for the prior degrees of freedom assigned to the slide and experiment effect variance parameters, ${\phi }_{jg}^2$ and ${\sigma }_{jg}^2$, respectively, for the two-study and five-study simulation data sets with medium mean ${\tau }_g^2$ = 0.3 (differentially expressed); 0.03 (non-differentially expressed) and simulated percent differentially expressed genes p_s = 10%. Shown are true integration-driven discovery rate (tIDR) and true integration-driven revision rate (tIRR) for threshold value of posterior probability of differential expression γ = 0.95, and the number of true discovered genes for posterior expected false discovery rate peFDR = 5%, for the Bayesian standardized expression integration (SEI) and probability integration (PI) models.

Two-Study Simulation Data		True Integration-Driven Discovery Rate, γ = 0.95		True Integration-Driven Revision Rate, γ = 0.95		True Genes, peFDR = 5%
Prior Degrees of Freedom
${\phi }_{jg}^2$	${\sigma }_{jg}^2$	SEI	PI	SEI	PI	SEI	PI
3	3	10.8%	16.2%	15.9%	4.5%	185	211
6	6	4.4%	11.9%	11.6%	1.2%	197	216
10	10	3.6%	10.2%	7.9%	0.6%	202	218
20	20	1.7%	8.1%	4.4%	0.5%	206	219
40	40	1.6%	6.6%	5.9%	0.5%	208	221
Five-Study Simulation Data
3	3	2.2%	15.2%	10.2%	3.6%	212	241
6	6	0%	8.8%	13.0%	2.8%	219	246
10	10	0%	6.9%	13.1%	2.7%	225	248
20	20	0%	3.9%	14.4%	3.1%	228	250
40	40	0%	5.1%	12.8%	1.8%	227	250