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