Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Table 5 Power calculations using functions in RNASeqPower

	Depth^a	PE CV^b	SE CV^c	FC^d	PE Power (n = 3)^e	SE Power (n = 3)^f	PE Power (n = 5)^e	SE Power (n = 5)^f
Exp 1	10	0.2074	0.2069	1.5	0.2589	0.2592	0.3956	0.3961
				2	0.6121	0.6127	0.8259	0.8264
Exp 2	10	0.1052	0.1007	1.5	0.3192	0.3215	0.4855	0.4887
				2	0.7215	0.7251	0.9080	0.9103
Exp 3	10	0.099	0.0907	1.5	0.3223	0.3262	0.4899	0.4955
				2	0.7264	0.7325	0.9111	0.9149
Exp 4	10	0.0264	0.0256	1.5	0.3464	0.3465	0.5241	0.5242
				2	0.7628	0.7630	0.9324	0.9325

^aAverage depth of coverage
^bBiological coefficient of variation derived from the estimateCommonDispersion function of edgeR for the PE data
^cBiological coefficient of variation derived from the estimateCommonDispersion function of edgeR for the SE data
^dFold change
^eThe power calculations performed for the PE data using the RNASeqPower package
^fThe power calculations performed for the SE data using the RNASeqPower package

ISSN: 1471-2164