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) |