Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

Table 2 Statistical analysis of DEGs from four normalization and test statistics given a nominal FDR ≤ 0.05. Listed are the number of TP and FP genes, the observed FDR and the PPV, sensitivity and specificity using MAQC datasets

Data	Statistical test (package)	Methods	# of TP	# of FP	PPV	Actual FDR	Sensitivity	Specificity
MAQC2 (n = 2)	Exact test (edgeR)	UQ-pgQ2	377	22	0.945	0.055	0.967	0.851
		TMM	384	81	0.826	0.174	0.985	0.453
		RLE	380	91	0.807	0.193	0.974	0.385
		UQ	379	92	0.805	0.195	0.972	0.378
	Wald test (DESeq2)	UQ-pgQ2	385	49	0.887	0.113	0.987	0.669
		UQ	374	80	0.824	0.176	0.959	0.460
		TMM	374	82	0.820	0.180	0.959	0.446
		RLE	376	83	0.819	0.181	0.964	0.439
	T-test (voom-limma)	UQ-pgQ2 & UQ	363	76	0.827	0.173	0.931	0.487
		TMM	373	97	0.794	0.206	0.956	0.345
		RLE	364	92	0.798	0.202	0.933	0.378
	QL F-test (edgeR)	UQ-pgQ2	387	59	0.868	0.132	0.997	0.587
		TMM	385	103	0.789	0.211	0.992	0.280
		RLE & UQ	385	108	0.781	0.219	0.992	0.245
MAQC3 (n = 5)	Exact test (edgeR)	UQ-pgQ2	383	51	0.882	0.118	0.987	0.643
		TMM	386	93	0.806	0.194	0.995	0.350
		RLE	386	98	0.798	0.202	0.995	0.315
		UQ	386	98	0.798	0.202	0.995	0.315
	Wald test (DESeq2)	UQ-pgQ2	384	83	0.822	0.178	0.990	0.420
		UQ	387	101	0.793	0.207	0.997	0.294
		TMM	386	103	0.789	0.211	0.995	0.280
		RLE	385	102	0.791	0.209	0.992	0.287
	T-test (voom-limma)	UQ-pgQ2 & UQ	362	58	0.862	0.138	0.932	0.594
		RLE	376	64	0.856	0.146	0.969	0.552
		TMM	350	60	0.853	0.146	0.902	0.580
	QL F-test (edgeR)	UQ-pgQ2	382	85	0.818	0.182	0.985	0.406
		TMM	385	99	0.796	0.205	0.992	0.308
		RLE	386	105	0.786	0.214	0.995	0.267
		UQ	386	104	0.788	0.212	0.995	0.273

ISSN: 1471-2164