Table 4

Power of different pathway enrichment methods

Pattern number

A

SEPEA_NT1

GSEA

Maxmean

SEPEA_NT2

SEPEA_NT3


1

0.01

0.05

328

610

188

510

52

357

686

321

2

0.01

0.05

271

505

189

508

37

295

580

39

3

0.01

0.05

344

692

222

496

32

347

712

480

4

0.01

0.05

166

361

212

468

32

157

379

11


Power estimates for the SEPEA_NT1, GSEA and SEPEA_NT2 methods (in terms of the number of experiments out of 1,000 that gave P-values for the randomization tests below nominal sizes of α = 0.01 and 0.05). The estimates for maxmean are given at an empirical size of 0.07 (nominal size of 0.001) and those for SEPEA_NT3 at an empirical size of 0.05 (nominal size of 0.001). These are results from simulations in which the treatment resulted in an over-expression of the mean expression of the target genes by the factor pert = 1.2. The methods were evaluated on correlation patterns 1-4.

Thomas et al. Genome Biology 2009 10:R44   doi:10.1186/gb-2009-10-4-r44

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