One of the proposed pathway scoring methods transforms the ranked gene p-values such that they follow a chi-squared distribution. The chi-squared distribution is a special case of the Gamma distribution with shape parameter 0.5. Thus we also examined whether using other shape parameters of the Gamma distribution could improve performance (see Methods, S12 and S13 Figs). This analysis suggested that the chi-squared pathway scoring method represents a good compromise for a wide range of genetic architectures.
