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Table 3 Differential expression

From: Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

  

Ovarian cancer

Gaucher

  

CM10

Q10

CM10/ Q10

 

label

Ciphergen A

43

19

57

57

 

Ciphergen B

37

15

47

46

 

Ciphergen C

41

13

50

30

chip

Ciphergen A

6

57

69

8

 

Ciphergen B

10

35

52

7

 

Ciphergen C

0

15

16

10

label:chip

Ciphergen A

0

0

0

3

 

Ciphergen B

0

0

0

0

 

Ciphergen C

0

0

0

0

label

Cromwell A

153

17

142

43

 

Cromwell B

112

12

95

40

 

Cromwell C

67

8

61

29

chip

Cromwell A

0

0

0

22

 

Cromwell B

0

0

0

37

 

Cromwell C

0

0

0

26

label:chip

Cromwell A

0

0

0

1

 

Cromwell B

0

0

0

0

 

Cromwell C

0

0

0

0

  1. Number of peaks with an adjusted p-value < 0,2 (ANOVA and correction for multiple testing) for different peak detection settings (A-C for both Ciphergen and Cromwell) for CM10, Q10, and CM10/Q10 (ovarian cancer dataset) and the Gaucher dataset. An ANOVA was performed for label effect (patient versus control), chip (array) effect and interaction effect label:chip.
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