Table 2.

Total error rate (%) and power (%) for alternative methods of microarray analysis for cases given in Table 1.

Case	Method
	FDR		pFDR		SAM		MD-MM
	Errors	Power	Errors	Power	Errors	Power	Errors	Power
1	10	0	10	0	9.6	3.6	9.0	9.8
2	8.1	19.6	8.1	20	7.5	25.5	6.5	35.4
3	6.8	33.2	6.7	34.4	3.9	61	3.8	63.9
4	10	0	10	0	10	0	5.8	43.8
5	50	0	49.9	0.1	48.2	3.7	40.1	17.1
6	35.2	30.5	33.8	33.8	32.2	36.5	26.2	49.4
7	24.4	52.6	21.9	58.9	23.1	55.1	14.6	72.8
8	50	0	50	0	50	0	24.7	51.8
9	50	0	50	0	49.9	0.1	22.1	56.9
10	49	2	48.9	2.2	48.8	2.5	18.6	64.1
11	45.9	8.3	45.3	9.7	42.5	15.4	12.2	77.8
12	50	0	50	0	50	0.1	15.0	71.8
13	50	0	49.8	0.4	42.4	15.6	35.8	31.3
14	29	43.2	27.3	47.3	25.7	50.6	21.9	58.5
15	24.2	52.8	21.8	58.9	19.7	63.2	14.8	72.4
16	50	0	50	0	50	0	22.6	56.3
Ave	33.9	15.6	33.3	17.4	32.1	20.4	18.2	52.5

^*Power=100[1−(# false negatives/# true DE)]

Errors=100(# false positives + # false negatives)/N.

For MD-MM, the null distribution was always defined as the distribution centered at 0 with smallest variance, genes in all other distributions were declared DE.