Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets

BMC Bioinformatics

Table 4 Comparison of geneset differential expression analysis method performances, based on the simulation model proposed by M Ackerman

		Cut-Off		a2.fixed	faeri. fixed.null	faeri. fixed.perms	GSA. mean*	GSA. absmean*	GSA. maxmean*	Globaltest. asymptotic	Globaltest. gamma	Globaltest. permutations	Gsea. pval	Gsea. fdr	Samgs. pval	Samgs. qval
		0.001	Set3	0	0	0	0	0	0	0	0	0	0	0	0	1
H ₀		0.01	Set3	1	0	0	0	0	0	0	0	0	0	0	0	2
		0.1	Set3	3	3	3	12	0	0	2	5	3	2	1	2	27
		0.001	Set2	100	96	97	15	25	12	54	96	95	69	20	91	94
	100% DE	0.01	Set2	100	99	99	15	25	12	95	99	97	99	77	98	99
Uni		0.1	Set2	100	100	100	78	72	64	99	99	99	100	100	99	100
		0.001	Set5	72	40	36	0	2	0	3	64	49	14	2	39	56
	50% DE	0.01	Set5	89	75	78	0	2	0	42	89	84	42	25	81	84
		0.1	Set5	100	94	94	7	17	3	93	99	98	93	84	96	99
		0.001	Set1	86	62	60	1	2	2	1	10	8	2	0	7	13
	100% DE	0.01	Set1	89	69	70	1	2	2	20	35	25	16	3	23	41
Uni+Cor		0.1	Set1	95	80	80	11	23	11	58	59	58	46	47	56	73
		0.001	Set4	55	43	39	0	0	0	0	15	7	4	3	4	11
	50% DE	0.01	Set4	65	52	54	0	0	0	18	30	24	13	14	23	43
		0.1	Set4	81	65	65	1	13	1	56	60	57	43	47	56	73
		0.001	Set7	0	100	100	1	67	40	100	100	100	1	0	100	100
	100% DE	0.01	Set7	0	100	100	1	67	40	100	100	100	10	1	100	100
Bidir		0.1	Set7	6	100	100	22	98	82	100	100	100	69	32	100	100
		0.001	Set9	0	84	82	0	7	2	32	95	93	0	0	86	93
	50% DE	0.01	Set9	0	95	95	0	7	2	93	100	100	1	0	100	100
		0.1	Set9	9	100	100	16	48	15	100	100	100	27	8	100	100
		0.001	Set6	0	84	84	0	11	8	5	28	17	6	1	15	25
	100% DE	0.01	Set6	0	88	89	0	11	8	39	50	43	17	8	43	61
Bidir+Cor		0.1	Set6	2	93	93	35	49	54	79	79	78	57	42	78	88
		0.001	Set8	0	63	62	0	2	1	3	30	14	0	0	13	23
	50% DE	0.01	Set8	0	75	76	0	2	1	36	50	42	3	0	40	58
		0.1	Set8	3	86	86	28	27	12	75	78	75	31	15	76	85

Each set of measurements presented was generated 100 times. The measurements in the table show, for each method, the number of detections of the different sets of measurements defined. The upper part of the table presents the results for unidirectional genesets only (all members over expressed) and the lower part concerns groups with a simulated mixed answer (over and under expression). The data related to H₀ shows the number of genesets detected by chance (false positives).

ISSN: 1471-2105