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Table 2 Number of TP and FP genes based on P-value ranking.

From: On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

 

σ μ

σ wtrep

 

Concentration (in pM)

TP

FP

TP

FP

No. of common TP

0.01 vs 0

0

34

0

34

0

0.03 vs 0.01

0

34

0

34

0

0.1 vs 0.03

7

27

9

25

7

0.3 vs 0.1

14

20

22

12

14

1 vs 0.3

30

4

33

1

30

3 vs 1

30

4

34

0

30

10 vs 3

33

1

34

0

33

30 vs 10

34

0

34

0

34

100 vs 30

33

1

34

0

33

300 vs 100

4

30

26

8

4

1000 vs 300

9

25

16

18

8

  1. The first column indicates the 11 test cases of pair-wise treatment conditions. The second and third columns indicate the number of TP and FP genes respectively for using σ μ as the summary statistic. Similarly, column four and five indicate the results for using σ wtrep . The last column indicates the result for the number of common TP genes found by both σ μ and σ wtrep .