Table 7

Comparison of the full, selected and successful group of gene sets

Group

Selection

Statistic

Nominal size

Effective size

PCA 50% var

PCA 90% var


Full

None

mean

71.7±1.7

40.9±0.7

4.4±0.03

16.7±0.14


median

37.0

28.1

4.1

15.3

Selected

all

mean

62.5±2.7

47.8±1.9

3.8±0.08

15.1±0.35

median

33.5

27.0

3.4

13.4

Global

median

32.0

25.5

3.3

12.8

GSEA

median

34.0

27.0

3.4

13.7

SAM-GS

median

40.5

28.0

3.7

14.3


Successful

all

mean

56.9±4.4

39.2±2.9

4.3±0.14

14.7±0.56

median

31.0

21.0

3.9

12.6

Global

median

22.0

18.5

3.8

11.7

GSEA

median

37.0

27.5

4.3

14.2

SAM-GS

median

30.5

22.5

4.0

12.7


Mean and median sizes of gene sets partitioned into three groups (see Section Successful gene sets for details.)

Holec et al. BMC Bioinformatics 2012 13(Suppl 10):S15   doi:10.1186/1471-2105-13-S10-S15

Open Data