Table 1

True positive rate of each EBV cell followed by different normalizations

Real aberrationsa

Global loess

CGHnormaliter

Poplowess

Haarseg

CG probeA

CG

CA

CGACBS

Channel clone


Cell 617, 14 M, 18p ter del

0

13.62

13.72

13.56

14.18

14.86

12.05

14.18

11.99

Cell 1151, 9.3 M, 18p, dup

0

0

0

9.04

8.87

6.21

9.06

8.92

8.87

Cell 1151, 1.7 M, 20p ter del

1.70

1.70

1.70

0

1.70

1.70

0

1.70

0

Cell 1151, monosomy X

151.87

151.87

151.87

151.59

151.87

151.87

151.87

151.87

151.87

Cell 1160, 3 M, 11 qter del

2.22

1.73

2.56

0

2.20

2.22

0

2.22

2.56

Cell 1162, 47.5 M, 14q dup

0

0

0

40.14

31.97

45.78

47.39

39.47

47.39

Cell 1162, 58 M, chr X, del

59.94

59.94

59.94

0

59.93

59.93

57.30

59.92

57.30

Cell 1168, trisomy 21

0

0

0

0

0

0

0

0

36.99

TPR

0.66

0.71

0.71

0.66

0.83

0.86

0.86

0.86

0.98


aValidated by Affymetrix 250 K array using genomic DNA. The first column represents the true validated aberrations of each EBV cell, followed by the detected aberration length after global loess, CGHnormaliter, poplowess, Haarseg, CGprobeA, CG, CA, CGACBS and channel clone normalization methods. The column with bold numbers shows the detected aberration length and true positive rate after the channel clone normalization. CA, channel standardization followed by recurrent genome artifact correction without CBS segmentation; CG, channel standardization followed by genome composition correction using enlarged window GC contents; CGACBS, channel standardization followed by genome composition correction using enlarged window GC contents and recurrent genome artifact correction with CBS segmentation; CGprobeA, channel standardization followed by genome composition correction using probe GC contents and recurrent genome artifact correction without CBS segmentation; Channel clone, channel standardization followed by genome composition correction using enlarged window GC contents and recurrent genome artifact correction without CBS segmentation.

Cheng et al. Genome Biology 2011 12:R80   doi:10.1186/gb-2011-12-8-r80

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