Enrichment methods comparison

Question

[coralieludwig]

Hi :)

I'm working on a python script that implements 3 enrichment analysis methods. In case of "enrichment" is not obvious, it is a question of comparing a query genes set to target genes sets gathered with a cross checking method (membership of a same metabolic path in my case).

Now I'd like to compare these methods to find the more appropriate one. However, one of these methods returns a p-value (Chi²) while an other returns a ratio (fraction that is common between the target and the query set). So how could I compare them ?

Thanks !