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Table 1 Simulation results for simulation studies 1, 2, 3, and 4 with number of replicates 4, 5, and 6, respectively

From: Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously

Study

Rep

True positives

Actual FDR

AUC

  

(Total positives)

(SD)

(SD)

  

Limma

edgeR

Proposed

Limma

edgeR

Proposed

Limma

edgeR

Proposed

1

4

1.34

10.32

194.92

0.0000

0.0518

0.0484

0.6141

0.6038

0.8332

  

(1.34)

(10.92)

(207.26)

(0.0000)

(0.0619)

(0.0287)

(0.0117)

(0.0102)

(0.0093)

 

5

1.04

6.32

294.38

0.0100

0.0291

0.0409

0.6105

0.5946

0.8541

  

(1.06)

(6.60)

(307.54)

(0.0707)

(0.0591)

(0.0155)

(0.0122)

(0.0117)

(0.0083)

 

6

0.96

4.62

361.04

0.0000

0.0445

0.0420

0.6053

0.5839

0.8676

  

(0.96)

(4.80)

(377.26)

(0.0000)

(0.1230)

(0.0138)

(0.0107)

(0.0097)

(0.0075)

2

4

0.60

2.82

26.44

0.0000

0.0632

0.0192

0.5771

0.5925

0.7554

  

(0.60)

(3.08)

(27.46)

(0.0000)

(0.1295)

(0.0310)

(0.0122)

(0.0094)

(0.0112)

 

5

0.50

1.76

86.90

0.0200

0.0857

0.0313

0.5675

0.5804

0.7698

  

(0.52)

(2.04)

(89.88)

(0.1414)

(0.2062)

(0.0220)

(0.0109)

(0.0100)

(0.0076)

 

6

0.16

1.08

136.00

0.0000

0.0367

0.0265

0.5617

0.5721

0.7792

  

(0.16)

(1.14)

(139.78)

(0.0000)

(0.1625)

(0.0155)

(0.0105)

(0.0105)

(0.0093)

3

4

1.10

8.94

129.22

0.0067

0.0421

0.0373

0.6277

0.6474

0.8359

  

(1.12)

(9.32)

(137.30)

(0.0471)

(0.0743)

(0.0322)

(0.0107)

(0.0122)

(0.0072)

 

5

0.68

9.02

239.14

0.0000

0.0346

0.0393

0.6176

0.6413

0.8551

  

(0.68)

(9.32)

(249.58)

(0.0000)

(0.0817)

(0.0161)

(0.0110)

(0.0122)

(0.0098)

 

6

0.66

6.94

331.44

0.0000

0.0381

0.0408

0.6158

0.6446

0.8731

  

(0.66)

(7.14)

(345.90)

(0.0000)

(0.1041)

(0.0136)

(0.0096)

(0.0095)

(0.0061)

4

4

0.72

7.68

121.68

0.0000

0.0554

0.0378

0.6083

0.6101

0.8069

  

(0.72)

(8.12)

(128.50)

(0.0000)

(0.0913)

(0.0293)

(0.0106)

(0.0122)

(0.0105)

 

5

0.94

5.86

211.54

0.0000

0.0326

0.0346

0.6035

0.6036

0.8257

  

(0.94)

(6.12)

(219.70)

(0.0000)

(0.0711)

(0.0166)

(0.0094)

(0.0107)

(0.0080)

 

6

0.66

4.06

296.70

0.0200

0.0290

0.0356

0.5966

0.5976

0.8410

  

(0.68)

(4.20)

(307.96)

(0.1414)

(0.1022)

(0.0132)

(0.0104)

(0.0101)

(0.0074)

  1. Summary statistics including number of true positives with total number of positives in parentheses, the actual FDR by controlling FDR at 0.05 level and its standard error in parentheses, and the area under ROC curve with standard error in parentheses