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 (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.

Kim et al. BMC Bioinformatics 2011 12:305   doi:10.1186/1471-2105-12-305

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