I am trying to find perturbed pathway from expression date using a kegg gene set.
In the GAGE paper (Luo et al., 2009), iit is recommanded to use the option same.dir=F on KEGG pathwayt is worthy to run gage with to capture pathways perturbed towards both directions simultaneously.
With the option same.dir=F, I only get in the results the part "greater", but when I use same.dir =F, I have completely different pathways and i have a part "greater" and a part "less".
I don't know how to interpret these results.
Using same.dir=F, how can i know if the pathway is upregulated or downregulated ? why do I get different results changing this option?
Thank you for your response