From: TCC: an R package for comparing tag count data with robust normalization strategies
DE method | edgeR | edgeR | edgeR | DESeq | DESeq | DESeq | baySeq | baySeq | baySeq |
---|---|---|---|---|---|---|---|---|---|
P G1 | 50% | 70% | 90% | 50% | 70% | 90% | 50% | 70% | 90% |
(a) TMM | |||||||||
PDEG = 5% | 90.30 | 90.30 | 90.18 | 89.09 | 89.08 | 88.92 | 89.43 | 89.42 | 89.22 |
PDEG = 15% | 90.30 | 90.12 | 89.63 | 89.15 | 88.91 | 88.26 | 89.54 | 89.28 | 88.66 |
PDEG = 25% | 90.40 | 89.89 | 88.26 | 89.27 | 88.62 | 86.82 | 89.63 | 89.07 | 87.25 |
(b) DEGES/TbT | |||||||||
PDEG = 5% | 90.30 | 90.31 | 90.28 | 89.09 | 89.12 | 89.07 | 89.43 | 89.47 | 89.41 |
PDEG = 15% | 90.30 | 90.25 | 90.26 | 89.15 | 89.07 | 89.01 | 89.54 | 89.48 | 89.49 |
PDEG = 25% | 90.41 | 90.27 | 89.89 | 89.27 | 89.07 | 88.61 | 89.63 | 89.56 | 89.22 |
(c) DEGES/edgeR | |||||||||
PDEG = 5% | 90.29 | 90.32 | 90.28 | 89.09 | 89.13 | 89.08 | 89.43 | 89.48 | 89.41 |
PDEG = 15% | 90.30 | 90.25 | 90.26 | 89.15 | 89.07 | 89.02 | 89.54 | 89.48 | 89.50 |
PDEG = 25% | 90.40 | 90.28 | 89.91* | 89.27 | 89.08 | 88.64 | 89.63 | 89.56 | 89.24 |
(d) iDEGES/edgeR | |||||||||
PDEG = 5% | 90.29 | 90.32 | 90.28 | 89.09 | 89.13 | 89.08 | 89.43 | 89.48 | 89.42 |
PDEG = 15% | 90.30 | 90.25 | 90.29* | 89.15 | 89.08 | 89.06 | 89.54 | 89.49 | 89.54 |
PDEG = 25% | 90.40 | 90.30* | 90.04* | 89.27 | 89.11 | 88.80 | 89.63 | 89.60 | 89.42 |
(e) iDEGES/TDT | |||||||||
PDEG = 5% | 90.30 | 90.32 | 90.28 | 89.09 | 89.12 | 89.09 | 89.43 | 89.48 | 89.42 |
PDEG = 15% | 90.30 | 90.23 | 90.20 | 89.15 | 89.05 | 88.93 | 89.54 | 89.45 | 89.40 |
PDEG = 25% | 90.40 | 90.25 | 89.82 | 89.27 | 89.04 | 88.53 | 89.63 | 89.52 | 89.13 |
(f) iDEGES/DESeq | |||||||||
PDEG = 5% | 90.30 | 90.31 | 90.28 | 89.09 | 89.13 | 89.09 | 89.43 | 89.48 | 89.43 |
PDEG = 15% | 90.30 | 90.24 | 90.21 | 89.15 | 89.05 | 88.95 | 89.54 | 89.45 | 89.42 |
PDEG = 25% | 90.40 | 90.26 | 89.86 | 89.27 | 89.05 | 88.58 | 89.63 | 89.53 | 89.18 |