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Table 7 Statistical significance between two methods for Datasets 3–38

From: A weighted average difference method for detecting differentially expressed genes from microarray data

a) MAS

 

Inferior

  

WAD

AD

FC

RP

modT

samT

shrinkT

ibmT

Superior

WAD

-

2.1E-07

6.7E-07

2.3E-06

2.2E-02

1.7E-02

2.0E-02

1.8E-01

 

AD

1.0E+00

-

8.1E-01

2.9E-04

1.0E+00

1.0E+00

1.0E+00

1.0E+00

 

FC

1.0E+00

1.9E-01

-

2.6E-04

1.0E+00

1.0E+00

1.0E+00

1.0E+00

 

RP

1.0E+00

1.0E+00

1.0E+00

-

1.0E+00

1.0E+00

1.0E+00

1.0E+00

 

modT

9.8E-01

8.6E-04

4.0E-03

1.4E-04

-

4.7E-01

9.0E-01

1.0E+00

 

samT

9.8E-01

2.5E-04

2.0E-03

6.6E-05

5.3E-01

-

6.9E-01

1.0E+00

 

shrinkT

9.8E-01

4.0E-04

2.2E-03

9.0E-05

1.0E-01

3.1E-01

-

1.0E+00

 

ibmT

8.2E-01

4.7E-05

2.6E-04

2.6E-05

2.2E-04

2.3E-03

2.9E-04

-

(b) RMA

 

Inferior

  

WAD

AD

FC

RP

modT

samT

shrinkT

ibmT

Superior

WAD

-

9.8E-01

9.8E-01

8.9E-01

3.0E-01

3.1E-01

2.5E-01

4.4E-01

 

AD

2.3E-02

-

4.7E-01

8.3E-02

9.2E-03

1.1E-02

7.2E-03

2.8E-02

 

FC

2.4E-02

5.3E-01

-

8.8E-02

1.1E-02

1.3E-02

8.4E-03

3.1E-02

 

RP

1.1E-01

9.2E-01

9.1E-01

-

8.4E-02

9.7E-02

6.6E-02

1.7E-01

 

modT

7.0E-01

9.9E-01

9.9E-01

9.2E-01

-

5.6E-01

6.5E-02

1.0E+00

 

samT

6.9E-01

9.9E-01

9.9E-01

9.0E-01

4.4E-01

-

2.1E-01

8.3E-01

 

shrinkT

7.5E-01

9.9E-01

9.9E-01

9.3E-01

9.4E-01

7.9E-01

-

1.0E+00

 

ibmT

5.6E-01

9.7E-01

9.7E-01

8.3E-01

3.2E-03

1.7E-01

1.9E-03

-

(c) DFW

 

Inferior

  

WAD

AD

FC

RP

modT

samT

shrinkT

ibmT

Superior

WAD

-

1.0E+00

1.0E+00

1.0E+00

1.3E-01

1.2E-01

4.5E-01

1.6E-01

 

AD

2.5E-03

-

1.6E-01

9.6E-01

5.1E-02

4.7E-02

2.1E-01

6.9E-02

 

FC

2.6E-03

8.4E-01

-

9.6E-01

5.1E-02

4.7E-02

2.1E-01

6.9E-02

 

RP

8.7E-04

4.2E-02

4.1E-02

-

3.0E-02

3.0E-02

1.1E-01

4.4E-02

 

modT

8.7E-01

9.5E-01

9.5E-01

9.7E-01

-

8.6E-02

9.9E-01

8.5E-01

 

samT

8.8E-01

9.5E-01

9.5E-01

9.7E-01

9.1E-01

-

9.9E-01

1.0E+00

 

shrinkT

5.5E-01

7.9E-01

7.9E-01

8.9E-01

6.1E-03

1.0E-02

-

2.6E-02

 

ibmT

8.4E-01

9.3E-01

9.3E-01

9.6E-01

1.5E-01

5.2E-04

9.7E-01

-

  1. The p-values between the 36 AUC values from a possibly superior method and those from a possibly inferior method were calculated by a one-tail paired t-test. The null hypothesis is that the mean of the 36 AUC values for one method is the same as that for the other method. There are two p-values for two methods compared. For example, in (a) MAS-preprocessed data, the p-value is 1.8E-01 when the alternative hypothesis is that the mean of the 36 AUC values for WAD is greater than that for ibmT while the p-value is 8.2E-01 when the alternative hypothesis is that the mean of the 36 AUC values for ibmT is greater than that for WAD. Combinations having p < 0.05 are highlighted in bold.
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Algorithms for Molecular Biology

ISSN: 1748-7188