Table 1

Summary of comparing the duplicate tumour samples as a repeated dataset (A and B) to assess the reproducibility of gene-lists.

A

B

A & B overlap

consensus (%)


Limma

QN

192

30

23

11.6

MC

225

222

59

15.2

CB

260

211

188

66.4


SAM

QN

214

40

30

13.4

MC

240

238

65

15.7

CB

265

218

193

66.6


Limma + UHRR

QN

205

31

24

11.3

MC

8

92

7

7.5

CB

144

119

112

74.2


SAM + UHRR

QN

224

42

32

13.7

MC

17

100

12

11.4

CB

149

125

117

74.5


Differentially expressed genes were identified using Limma and SAM as described in the text with quantile-normalisation (QN), mean-centring (MC), and ComBat (CB). The UHRR was used as an inter-batch calibrator.

Kitchen et al. BMC Genomics 2010 11:134   doi:10.1186/1471-2164-11-134

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