Table 3 Comparison results of various methods for SELC dataset on calculated log 2 fold change of gene expression
From: Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate
Comparison | Gene | qRT-PCR | Cufflinks | RSEM | MMSEQ | NLDMseq |
|---|---|---|---|---|---|---|
S vs. NS | S100A8 | +1.15 | +1.13(0.02) | +2.72(1.38) | +3.20(1.78) | +1.65(0.44) |
S100A9 | +0.83 | +1.69(1.03) | +1.79(1.16) | +1.86(1.24) | +1.75(1.10) | |
CYP4F2 | +1.27 | +4.12(2.24) | +3.59(1.82) | +9.51(6.49) | +2.09(0.64) | |
C vs. NC | CCL20 | +4.01 | +6.00(0.50) | +4.66(0.16) | +5.32(0.32) | +7.08(0.76) |
IL8 | +1.50 | +1.51(0.01) | +1.21(0.19) | +1.67(0.11) | +1.05(0.30) | |
SCGB3A1 | +0.51 | +1.65(2.23) | +1.76(2.45) | +1.85(2.63) | +1.82(2.57) | |
SCGB1A1 | −0.48 | +1.37(3.89) | +1.56(4.26) | +1.02(3.13) | +1.62(4.39) | |
Average AER | NA | 1.42 | 1.63 | 2.24 | 1.46 | |