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Table 2 Summarized metrics for analyzed pipelines based on a simulation dataset

From: A benchmark for RNA-seq quantification pipelines

Method

SD low

SD medium

SD high

NE (K = 1)

NN (K = 1)

TxDiff low

TxDiff medium

TxDiff high

deFC low

deFC medium

deFC high

pAUC

Cufflinks

0.73 (0.002)

0.54 (0.003)

0.26 (0.001)

0.090

0.657

0.34 (0.011)

0.08 (0.003)

0.05 (0.003)

0.53 (0.009)

0.95 (0.006)

0.98 (0.003)

0.61

eXpress

0.71 (0.003)

0.67 (0.004)

0.30 (0.001)

0.09

0.68

0.33 (0.009)

0.07 (0.003)

0.07 (0.003)

0.47 (0.011)

0.87 (0.015)

0.91 (0.012)

0.60

Flux Capacitor

1.03 (0.004)

1.23 (0.007)

0.40 (0.002)

0.15

0.63

0.46 (0.013)

0.15 (0.006)

0.07 (0.004)

0.39 (0.011)

0.82 (0.013)

0.97 (0.009)

0.52

Kallisto

0.72 (0.003)

0.55 (0.003)

0.27 (0.001)

0.10

0.63

0.37 (0.011)

0.08 (0.004)

0.05 (0.003)

0.56 (0.008)

0.95 (0.006)

0.98 (0.002)

0.58

RSEM

0.65 (0.002)

0.48 (0.003)

0.25 (0.001)

0.08

0.69

0.43 (0.011)

0.07 (0.004)

0.04 (0.003)

0.58 (0.008)

0.96 (0.006)

1.00 (0.003)

0.65

Sailfish

0.76 (0.003)

0.65 (0.004)

0.30 (0.001)

0.11

0.57

0.34 (0.009)

0.08 (0.004)

0.05 (0.003)

0.52 (0.011)

0.94 (0.011)

0.96 (0.006)

0.56

Salmon

0.64 (0.002)

0.52 (0.003)

0.26 (0.001)

0.09

0.67

0.35 (0.010)

0.08 (0.004)

0.05 (0.003)

0.54 (0.008)

0.95 (0.007)

1.00 (0.003)

0.61

  1. The last four columns are based on differential expression of transcripts. pAUC partial area under the receiver operating characteristic curve