Table 1.

Performance Comparison on the simulated mRNA-Seq data

Algorithms	Condition	IsoformEx	RSEM [21] (v1.1.8) with default parameters	Cufflinks [20] (v0.9.3) (--min-isoform-fraction 0)
The number of estimated transcripts (n)	vest ≥ 0	55416	55441	55441
	vest > 0.01	35064	25967	25839
	vest ≥ 0	8.41 × 10-6	1.02 × 10-5	9.23 × 10-6
	vest > 0.01	1.32 × 10-5	2.15 × 10-5	1.96 × 10-5
r = Corr(vtrue , vest )	vest ≥ 0	0.921	0.839	0.913
	vest > 0.01	0.920	0.838	0.912

Estimation error and correlation coefficient between estimated expression levels (v_est) and known true expression levels (v_true) for our simulated dataset when all estimated transcripts (v_est ≥ 0) were considered or some expressed transcripts (v_est > 0.01) were only considered. p_true (i) denotes the i-th element of the proportion vector of true expression values (p_true = v_true/∑ v_true), and p_est (i) denotes the i-th element of the proportion vector of estimated expression values (p_est = v_est/∑ v_est). The error was defined as the mean value of absolute difference between the true proportion vector and the proportion vector of the estimated values.