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Table 1 ComBat (ChAMP) applied to increasing sample sizes

From: Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies

sample size

batch factors

balanced

random

unbalanced

mean-p

λ+

FDR*

BF**

mean-p

λ+

FDR*

BF**

mean-p

λ+

FDR*

BF**

n = 48

8 rows + 6 chips

0.4131827

1.720126

3540

15

0.3735538

1.990719

27,057

132

0.2872

3.880235

156,084

2803

n = 96

8 rows + 12 chips

0.4395739

1.465350

265

4

0.4254060

1.538365

1412

19

0.2609

4.999723

214,009

11,048

n = 144

8 rows + 18 chips

0.4487983

1.391675

84

2

0.4308005

1.453891

1218

8

0.2335

6.362690

273,773

25,522

n = 192

8 rows + 24 chips

0.4533012

1.355385

47

6

0.4438228

1.428494

218

2

0.2133315

7.746447

318,618

42,427

n = 240

8 rows + 30 chips

0.4565824

1.334509

27

1

0.4424769

1.419485

226

4

0.1978271

9.738140

352,805

59,949

n = 288

8 rows + 36 chips

0.4588096

1.320805

9

2

0.4443718

1.406706

181

4

0.1854536

11.319961

379,740

77,903

n = 336

8 rows + 42 chips

0.4580821

1.310937

11

2

0.4453380

1.388399

144

4

0.1733198

13.128076

406,856

97,847

n = 384

8 rows + 48 chips

0.4589804

1.303460

28

1

0.4512571

1.370874

41

3

0.1574975

15.871418

440,828

127,703

n = 432

8 rows + 54 chips

0.4609161

1.296584

2

0

0.4532645

1.360342

84

4

0.1565864

16.385741

442,872

130,896

n = 480

8 rows + 60 chips

0.4629813

1.290615

0

0

0.4545829

1.352150

77

3

0.1495949

18.068155

457,389

146,684

n = 528

8 rows + 66 chips

0.4640470

1.286172

4

1

0.4541513

1.347141

89

4

0.1444482

19.435062

469,246

159,929

n = 576

8 rows + 72 chips

0.4643993

1.282560

5

0

0.4562415

1.346690

67

3

0.1392911

21.116253

480,228

174,133

n = 624

8 rows + 78 chips

0.4647209

1.279449

1

1

0.4546367

1.351416

97

3

0.1319790

22.583813

495,269

193,145

n = 672

8 rows + 84 chips

0.4646304

1.277031

10

0

0.4550306

1.344902

99

1

0.1285275

24.769395

501,777

201,233

n = 720

8 rows + 90 chips

0.4629008

1.275070

5

1

0.4552286

1.342806

94

3

0.1250251

26.836670

509,759

213,140

n = 768

8 rows + 96 chips

0.4631314

1.273107

0

0

0.4545927

1.341437

118

3

0.1209156

28.445529

517,941

224,289

  1. + Genomic Inflation Factor λ
  2. * Significant CpG sites with False Discovery Rate 5%
  3. ** Significant CpG sites with Bonferroni correction 5%