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 (t IDR) and true integration-driven revision rate (t IRR) 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 pe FDR = 5%, for the Bayesian standardized expression integration (SEI) and probability integration (PI) models.

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