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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