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Table 3 POG values for the 100 top-ranked genes among six test sites

From: Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

Method

PLIER

VSN

FARMS

mmgMOS

MBEI

GCRMA

MAS

RMA

DFW

Sample A vs. B

         

WAD

64

56

71

65

69

58

61

62

60

AD

45

59

65

62

58

65

45

64

59

FC

40

60

65

60

58

65

45

64

59

RP

43

58

65

65

59

65

42

63

59

modT

1

22

0

3

15

5

6

1

1

samT

11

11

0

55

39

6

31

10

1

shrinkT

0

12

-

37

20

10

5

4

1

ibmT

-

21

0

-

15

15

8

3

1

Sample C vs. D

         

WAD

8

36

41

12

33

9

8

20

10

AD

1

6

17

13

4

4

1

4

4

FC

1

8

16

14

2

3

0

5

4

RP

2

10

17

12

4

3

1

5

4

modT

0

0

0

0

0

0

2

1

0

samT

2

0

0

13

1

0

3

3

0

shrinkT

0

0

-

0

2

0

0

1

0

ibmT

-

0

0

-

1

1

-

6

0

  1. Various POG values such as for FARMS/shrinkT could not be calculated because those statistics include infinities. Note POG values for MAS, RMA, and DFW-preprocessed data.
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Algorithms for Molecular Biology

ISSN: 1748-7188