Table 1.

Accuracy measures for quantification methods applied to simulated data

	SE			PE
Method	MPE	SE 10% EF	FP	MPE	PE 10% EF	FP
RSEM	3.1/4.1/7.1	14.1/25.1/44.1	0.9/1.7/12.0	3.1/4.0/5.2	14.4/23.3/35.7	1.0/1.8/11.3
IsoEM	4.6/5.6/8.0	18.1/29.0/45.4	1.7/3.2/31.3	4.0/4.8/5.1	16.9/25.5/35.3	1.2/1.7/11.1
Cufflinks	9.5/10.7/18.1	46.6/53.3/65.3	2.5/11.1/98.5	20.2/20.4/10.5	89.3/86.4/51.1	2.7/8.6/98.4
rQuant	8.9/12.6/43.9	44.4/58.9/89.0	7.0/16.9/99.1
RSEM v0.6	10.1/11.2/10.4	50.5/56.0/50.7	1.4/2.9/39.5

Accuracy of five RNA-Seq quantification methods on simulated SE and PE data. Values are given as gene/global isoform/within-gene isoform.