how to set cutoff for the gage enrichment results value of stat.mean

Question

[alwayshope]

Dear experts,

Do you have any idea which is a good cutoff for the enrichment results by gage package, is the abs(enrichment score/stat.mean) >=2 a good threshold?

It seems quite challenging when trying to display the enrichment pathways when filtering by q value < 0.05, with nearly nothing left, while if you filter by p-value < 0.05, there will be 70 or many more pathways items, which is not easy to display on one page. When you have multiple time points, and melt the data frame, the display can be much more challenging. Picture uploaded at https://ibb.co/bzrJYVY

Many thanks!