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Table 1 Average AUC values for simulation data with replicates

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

  1. Average AUC values (%) of 100 trials for each simulation condition are shown. Simulation data contain a total of 10,000 genes: PDEG% of genes is for DEGs, PG1% of PDEG in G1 is higher than in G2, and each group has three biological replicates (i.e., G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, and G2_rep3). A total of nine conditions (three PDEG values × three PG1 values) are shown. The highest AUC value for each condition is in bold. AUC values with asterisks indicate significant improvements (p-value < 0.01, paired t-test) compared with DEGES/TbT. We used a bootstrap resampling size of 10,000 in baySeq when performing the normalization (i.e., baySeq at step 2 in the DEGES/TbT) and 2,000 when performing the DEG identification after normalization (i.e., baySeq in the XXX-baySeq combination).