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Table 1 Percent of sets found as significant for the simulated data

From: Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16

 

FET

   
 

5.9

9.2

13.8

18.4

GSEA

SUMSQ

SUMSTAT

Pseudo-gene sets

       

   No associated genes

1.4

2.8

0.0

0.9

3.2

3.7

3.7

   1-9 weakly associated genes

9.8

3.3

1.6

3.3

8.5

8.2

8.2

   10+ weakly associated genes

10.6

7.7

1.9

1.9

11.5

11.5

15.4

   1-2 strongly associated genes, but no weakly associated genes

0.0

0.0

5.3

0.0

0.0

0.0

0.0

Real gene sets

       

   Many weakly associated genes

51.7

49.2

13.3

5.0

58.3

60.0

70.8

   Some strongly associated genes

2.5

3.8

7.5

33.8

6.3

36.3

23.8

   Null sets (no associated genes)

0.0

6.7

1.7

3.3

1.7

5.0

3.3