Evaluation of read count based RNAseq analysis methods

Guo, Yan; Li, Chung-I; Ye, Fei; Shyr, Yu

doi:10.1186/1471-2164-14-S8-S2

BMC Genomics

Table 2 Performance comparison under different scenarios

From: Evaluation of read count based RNAseq analysis methods

		FDR = 0.1			FDR = 0.05			FDR = 0.01
		N_s	FPR	TPR	N_s	FPR	TPR	N_s	FPR	TPR
I	DESeq	759	0.0090	0.6779	679	0.0054	0.6304	550	0.0020	0.5316
	Edger	825	0.0115	0.7216	740	0.0068	0.6799	614	0.0023	0.5934
	DEGseq	8814	0.8735	0.9532	8864	0.8573	0.8573	8415	0.8306	0.9402
	NBPSeq	1167	0.0480	0.7346	972	0.0322	0.6828	723	0.0153	0.5850
	Bayseq	729	0.0060	0.6750	654	0.0027	0.6296	543	0.0006	0.5384
	TSPM	2307	0.1687	0.7893	1815	0.0120	0.7306	1202	0.0663	0.6050
II	DESeq	289	0.0153	0.1515	175	0.0096	0.0890	59	0.0037	0.0255
	Edger	239	0.0138	0.1139	130	0.0080	0.0580	38	0.0028	0.0127
	DEGseq	8379	0.8292	0.9162	8215	0.8119	0.9081	7921	0.7801	0.8923
	NBPSeq	308	0.0207	0.1219	194	0.0134	0.0729	70	0.0054	0.0213
	Bayseq	189	0.0070	0.1260	88	0.0029	0.0617	10	0.0003	0.0067
	TSPM	291	0.0262	0.0557	262	0.0234	0.0513	217	0.0191	0.0447
III	DESeq	363	0.0056	0.6200	319	0.0034	0.5739	255	0.0013	0.4860
	Edger	401	0.0068	0.6729	354	0.0041	0.6301	284	0.0014	0.5414
	DEGseq	8451	0.8391	0.9598	8288	0.8222	0.9555	8002	0.7925	0.9462
	NBPSeq	567	0.0241	0.6767	474	0.0169	0.6283	346	0.0084	0.5335
	Bayseq	332	0.0031	0.6052	295	0.0015	0.5615	242	0.0004	0.4763
	TSPM	851	0.0529	0.6892	651	0.0354	0.6311	426	0.018	0.5035
IV	DESeq	758	0.0090	0.6770	678	0.0055	0.6290	544	0.0019	0.5269
	Edger	828	0.0117	0.7225	739	0.0068	0.6780	613	0.0023	0.5923
	DEGseq	9326	0.9297	0.9592	9081	0.9035	0.9494	8812	0.8748	0.9384
	NBPSeq	1860	0.1252	0.7333	1299	0.0707	0.6622	792	0.0277	0.5423
	Bayseq	728	0.0066	0.6686	653	0.0032	0.634	540	0.0008	0.5332
	TSPM	7387	0.3374	0.7515	3005	0.2575	0.6879	1931	0.1524	0.5593
V	DESeq	686	0.0084	0.6103	611	0.0050	0.5663	494	0.0018	0.4779
	Edger	747	0.0107	0.6507	667	0.0062	0.6109	549	0.0020	0.5315
	DEGseq	8763	0.8685	0.9454	8609	0.8520	0.9411	8354	0.8247	0.9312
	NBPSeq	1049	0.0431	0.6612	878	0.0293	0.6142	648	0.0139	0.5226
	Bayseq	667	0.0055	0.6186	598	0.0026	0.5746	493	0.0006	0.4886
	TSPM	2072	0.1488	0.7324	1617	0.1047	0.6747	1072	0.0575	0.5544
VI	DESeq	789	0.0086	0.6816	679	0.0051	0.6331	547	0.0018	0.5305
	Edger	825	0.0106	0.7301	741	0.0060	0.6869	615	0.002	0.5975
	DEGseq	8811	0.8721	0.9618	8675	0.8576	0.9567	8436	0.8318	0.9493
	NBPSeq	1070	0.0380	0.7283	910	0.0256	0.6790	689	0.022	0.5788
	Bayseq	722	0.0055	0.6727	646	0.0023	0.6254	535	0.0005	0.5310
	TSPM	1920	0.1277	0.7711	1485	0.0086	0.7067	950	0.0418	0.5736
VII	DESeq	233	0.0125	0.1211	144	0.0080	0.0725	53	0.0034	0.0220
	Edger	200	0.0121	0.0913	109	0.0070	0.0457	34	0.0026	0.0106
	DEGseq	8429	0.8346	0.9184	8255	0.8163	0.9091	7949	0.7840	0.8929
	NBPSeq	253	0.0170	0.0991	153	0.0108	0.0562	59	0.0047	0.0165
	Bayseq	156	0.0054	0.1076	70	0.0021	0.0508	7	0.0002	0.0047
	TSPM	296	0.0024	0.0571	266	0.0236	0.0537	219	0.0191	0.0476

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ISSN: 1471-2164

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