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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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BMC Bioinformatics

ISSN: 1471-2105

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