Table 3 Application of GSEA to the different RMA and fRMA pre-processing and data merging methods
Gene set | RMA | CB RMA | ZS RMA | fRMA | ||||
|---|---|---|---|---|---|---|---|---|
| Â | ES | p-value | ES | p-value | ES | p-value | ES | p-value |
EGF pathway | -0.4229 | 0.1285 | -0.4542 | 0.0923 | -0.4127 | -0.3109 | -0.3731 | 0.3145 |
Stathmin pathway | -0.4307 | 0.4712 | -0.4281 | 0.5079 | -0.2711 | -0.6063 | -0.2844 | 0.9051 |
Homologous recombination | 0.6766 | 0.0082 | 0.6956 | 0.0073 | 0.6962 | 0.0019 | 0.3378 | 0.5750 |
BRCA1 pathway | 0.2974 | 0.0278 | 0.3017 | 0.0403 | 0.2982 | 0.1353 | -0.1768 | 0.8875 |
HER2 pathway | 0.3388 | 0.5658 | 0.3475 | 0.5507 | 0.4504 | 0.0730 | -0.3795 | 0.4612 |