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Table 4 Comparison results of various methods for HBC dataset on calculated log 2 fold change of isoform expression

From: Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Comparison qRT-PCR Cufflinks RSEM MMSEQ NLDMseq
Case 1 −0.4 −0.81(1.03) −0.41(0.02) −0.74(0.85) −0.91(1.28)
Case 2 −0.5 −0.73(0.46) −0.83(0.66) −0.57(0.14) −0.59(0.18)
Case 3 −0.9 +4.52(6.02) +4.91(6.46) +4.42(6.02) −0.34(0.62)
Case 4 −1.0 +3.36(4.36) +4.44(5.44) +4.59(5.59) −0.04(0.96)
Case 5 −0.3 −1.74(4.80) −0.93(2.10) −1.29(3.30) −2.41(7.03)
Case 6 −1.0 −1.11(0.11) −0.71(0.29) −1.08(0.08) −1.29(0.29)
Case 7 +1.2 +1.12(0.07) +1.34(0.12) +1.47(0.23) +0.37(0.69)
Case 8 +1.0 +1.26(0.26) +1.56(0.57) +1.67(0.67) +1.37(0.37)
Case 9 −5.6 −5.70(0.02) −5.40(0.04) −5.50(0.02) −7.76(0.39)
Case 10 −4.5 −4.67(0.04) −4.71(0.05) −4.83(0.07) −5.61(0.25)
Case 11 +0.4 +0.52(0.30) 0.01(0.98) +0.34(0.15) +0.26(0.35)
Case 12 +1.5 +1.71(0.14) +0.81(0.46) +1.00(0.33) +2.38(0.59)
Case 13 −4.7 −2.74(0.42) −2.92(0.38) −4.28(0.09) −1.07(0.77)
Case 14 −5.2 −5.89(0.13) −4.51(0.13) −4.70(0.10) −4.26(0.18)
Case 15 −5.4 +3.57(1.66) +1.83(1.34) +1.79(1.33) −0.21(0.96)
Case 16 −5.9 +1.11(1.19) +0.21(1.04) +1.37(1.23) −3.33(0.44)
No. of inconsistency NA 4(1.31) 4(1.25) 4(1.26) 0(0.96)
  1. The symbol “ +” stands for up-regulation and “ −” for down-regulation. Numbers in the brackets stand for absolute error rates (AER) compared with qRT-PCR results. AER is calculated by |(re)/r|, where |·| stands for absolute, and r and e represent qRT-PCR and RNA-seq measurements, respectively. The last line shows the number of inconsistent regulation and the average AER for each method