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Table 1 Performance Comparison on the simulated mRNA-Seq data

From: IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from 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
  1. Estimation error and correlation coefficient between estimated expression levels (vest) and known true expression levels (vtrue) for our simulated dataset when all estimated transcripts (vest ≥ 0) were considered or some expressed transcripts (vest > 0.01) were only considered. ptrue (i) denotes the i- th element of the proportion vector of true expression values (ptrue = vtrue/∑ vtrue), and pest (i) denotes the i- th element of the proportion vector of estimated expression values (pest = vest/∑ vest). The error was defined as the mean value of absolute difference between the true proportion vector and the proportion vector of the estimated values.
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