Table 7.

Simulation study 2, with n_X=n_Y=30 and 100 runs

B	DE	10f0	C i	${\overline{n}}_i$	$\overline{\mathit{\text{OR}}}$	$\overline{\mathit{\text{FP}}}$	$\overline{\mathit{\text{dFP}}}$	$\overline{\mathit{\text{FPC}}}$
				(sd)	(sd)	(sd)	(sd)	(sd)
			$C_1^{\ast }$	27.9	160.4	6.6	8.1	32.0
				(31.2)	(102.2)	(1.1)	(10.8)	(43.9)
	5	9.1	C 2	92.1	10.1	9.0	24.1	100
				(25.5)	(0.8)	(0.4)	(4.0)	(0)
			C 3	82.5	7.8	9.4	41.6	100
				(17.9)	(0.3)	(0.3)	(2.2)	(0)
			$C_1^{\ast }$	20.0	233.0	0.0	0.0	0.0
				(0.0)	(35.1)	(0.0)	(0.0)	(0)
1	20	9.1	C 2	96.5	10.4	9.0	22.0	100
				(12.7)	(0.5)	(0.1)	(1.5)	(0)
			C 3	90.1	7.7	9.2	41.1	100
				(14.2)	(0.2)	(0.1)	(1.4)	(0)
			$C_1^{\ast }$	100.0	209.5	0.0	0.0	0.0
				(0.0)	(32.9)	(0.0)	(0.0)	(0)
	100	8.9	C 2	73.7	10.8	9.1	20.7	100
				(10.9)	(0.59)	(0.2)	(1.5)	(0)
			C 3	69.1	8.2	9.2	37.5	100
				(11.2)	(0.25)	(0.2)	(1.6)	(0)
			$C_1^{\ast }$	9.9	119.7	1.0	0.2	0.0
				(0.6)	(16.9)	(0.2)	(0.0)	(0.0)
	10	9.1	C 2	102.2	10.5	9.0	22.1	99.9
				(14.2)	(0.7)	(0.1)	(1.5)	(0.7)
			C 3	94.2	7.7	9.2	41.7	100
				(13.2)	(0.2)	(0.1)	(1.4)	(0.0)
			$C_1^{\ast }$	40.0	118.6	0.0	0.0	0.0
				(0.1)	(20.0)	(0.0)	(0.0)	(0.0)
2	40	9.1	C 2	97.0	10.3	9.1	22.2	100
				(12.0)	(0.5)	(0.1)	(0.4)	(0.0)
			C 3	87.4	7.7	9.2	41.2	100
				(12.9)	(0.2)	(0.1)	(1.2)	(0.0)
			$C_1^{\ast }$	115.9	120.1	0.0	0.0	0.0
				(38.9)	(18.9)	(0.0)	(0.0)	(0.0)
	200	8.6	$C_2^{\ast }$	95.3	72.7	1.6	3.7	16.7
				(15.5)	(31.3)	(3.5)	(8.2)	(37.8)
			C 3	118.5	8.9	9.3	31.2	100
				(28.3)	(0.5)	(0.1)	(3.2)	(0.0)
			$C_1^{\ast }$	14.6	86.2	0.26	0.09	0.0
				(1.14)	(14.1)	(0.31)	(0.11)	(0)
	15	9.0	C 2	103.9	9.0	8.4	22.1	99.6
				(11.8)	(0.13)	(0.48)	(1.5)	(1.1)
			C 3	92.8	7.2	9.2	41.6	100
				(10.7)	(0.77)	(0.13)	(1.4)	(0.0)
			$C_1^{\ast }$	59.9	81.2	0.03	0.03	0.0
				(0.29)	(12.1)	(0.07)	(0.06)	(0)
3	60	8.9	C 2	93.8	10.3	9.1	22.3	99.9
				(12.3)	(0.43)	(0.13)	(1.4)	(0.3)
			C 3	87.2	7.7	9.2	41.3	100
				(11.4)	(0.16)	(0.13)	(1.3)	(0.0)
			$C_1^{\ast }$	142.4	81.0	0.00	0.00	0.0
				(31.0)	(13.7)	(0.00)	(0.00)	(0)
	300	8.4	$C_2^{\ast }$	157.5	54.6	0.03	0.04	0.0
				(31.0)	(11.1)	(0.06)	(0.09)	(0)
			C 3	119.2	8.9	9.4	30.3	99.9
				(11.4)	(0.28)	(0.10)	(0.96)	(0.02)

Evaluation of the second step of the ORdensity method with α=0.05. In the first column number of blocks. In column 2, the number of total simulated DE genes. In column 3, the 10×f₀ values where f₀ is the average proportion of permuted cases in sets U_i. In column 4, the “*” indicates the clusters considered by the procedure. Columns 5–8 contain for each cluster: the mean number of genes (${\overline{n}}_i$), the mean of OR values ($\overline{\mathit{\text{OR}}}$), the mean of FP values ($\overline{\mathit{\text{FP}}}$), the mean of dFP values ($\overline{\mathit{\text{dFP}}}$). In the last column the mean of False Positives genes per cluster in % ($\overline{\mathit{\text{FPC}}}$). Corresponding standard deviations are in brackets