. Author manuscript; available in PMC: 2009 Aug 10.

Published in final edited form as: J Stat Plan Inference. 2008 Feb 1;138(2):387–404. doi: 10.1016/j.jspi.2007.06.007

Table 3.

Sensitivity analysis

Method	(n₁, n₂)	γ₀	Mean FNR	SD	Mean FPR	SD
Proposed criterion	(25, 25)	0.70	0.0000	0.0000	0.0963	0.1224
under model (2.5)		0.80	0.0000	0.0000	0.0202	0.0351
		0.90	0.0001	0.0023	0.0012	0.0021
SAM (FDR ≤ 0.05)			0.4290	0.1043	0.0014	0.0015
SAM (FDR ≤ 0.10)			0.2800	0.0834	0.0040	0.0024
PERMAX (α = 0.05)			0.8046	0.0556	0.0000	0.0002
PERMAX (α = 0.10)			0.7428	0.0621	0.0001	0.0003
EBarrays (PP > 0.5)			0.0000	0.0000	0.9999	0.0004
EBarrays (PP > 0.7)			0.0063	0.0128	0.8935	0.1248

Proposed criterion	(20, 20)	0.70	0.0000	0.0009	0.1217	0.1408
under model (2.5)		0.80	0.0001	0.0013	0.0286	0.0476
		0.90	0.0002	0.0018	0.0020	0.0040
SAM (FDR ≤ 0.05)			0.5992	0.0886	0.0011	0.0011
SAM (FDR ≤ 0.10)			0.4646	0.1042	0.0029	0.0021
PERMAX (α = 0.05)			0.8980	0.0430	0.0001	0.0003
PERMAX (α = 0.10)			0.8588	0.0501	0.0001	0.0003
EBarrays (PP > 0.5)			0.0001	0.0015	0.9997	0.0006
EBarrays (PP > 0.7)			0.0304	0.0381	0.6714	0.2652

Proposed criterion	(10, 10)	0.70	0.0024	0.0072	0.2145	0.2037
under model (2.5)		0.80	0.0058	0.0109	0.0718	0.1004
		0.90	0.0147	0.0180	0.0100	0.0170
SAM (FDR ≤ 0.05)			0.9176	0.0469	0.0007	0.0009
SAM (FDR ≤ 0.10)			0.8909	0.0685	0.0011	0.0012
PERMAX (α = 0.05)			0.9890	0.0141	0.0000	0.0002
PERMAX (α = 0.10)			0.9798	0.0194	0.0001	0.0003
EBarrays (PP > 0.5)			0.0027	0.0074	0.9970	0.0039
EBarrays (PP > 0.7)			0.4563	0.1507	0.0688	0.06111

Proposed criterion	(5, 5)	0.70	0.0265	0.0269	0.2989	0.2343
under model (2.5)		0.80	0.0510	0.0372	0.1301	0.1388
		0.90	0.0991	0.0478	0.0308	0.0334
SAM (FDR ≤ 0.05)			0.9724	0.0226	0.0011	0.0011
SAM (FDR ≤ 0.10)			0.9717	0.0252	0.0011	0.0012
PERMAX (α = 0.05)			0.9996	0. 0028	0.0000	0.0002
PERMAX (α = 0.10)			0.9990	0.0045	0.0001	0.0003
EBarrays (PP > 0.5)			0.0209	0.0316	0.9764	0.0335
EBarrays (PP > 0.7)			0.9020	0.1032	0.0067	0.0102