Table 4.

Results of hierarchical clustering on four cancer types

Experiment		Kallisto	Kallisto (bias)	Salmon	Salmon (bias)	eXpress	eXpress (bias)	RSEM	RSEM (bias)	BaseEM	IntMTQ
E1	ARI	0.032	0.135	0.209	0.150	0.142	0.171	0.092	0.067	0.152	0.251
	NMI	0.187	0.295	0.417	0.351	0.329	0.355	0.293	0.273	0.342	0.390
E2	ARI	0.267	0.267	0.267	0.267	0.267	0.267	0.267	0.267	0.267	0.310
	NMI	0.543	0.543	0.543	0.543	0.543	0.543	0.543	0.543	0.543	0.569
E3	ARI	0.094	0.272	0.252	0.171	0.137	0.035	0.137	0.095	0.137	0.158
	NMI	0.300	0.464	0.482	0.406	0.369	0.261	0.369	0.296	0.369	0.419

Note: (bias) means the baseline methods were performed with sequence-specific bias correction. The best results across the ten methods are bold.