Hello everyone !
I need your help, please.
I use ClusterProfiler (gseKEGG() function) to perform GSEA with 273 genes. Here my scenario:
I use 1000 permutation and exponent=1.
Genes expression are mesured after 24h and after 36h . At 24h there are more genes who are up/dow regulated. I got mTor SIgnaling pathway as up-enriched with a p-value =0.039 (Ok) but adjust.pvalue=0.36.
At 36h all genes are differenciel expressed and more of them are up-regulated. The gene upregulted most are the genes belon to mTor signalingpathway (at 24H) but its p-value is 0.23 and adust.pvalue is 0.72.
How can I interpret that ? With few DEG i fund a good p-value and when more gene are DE a have a non significance pvaue.
An other question : Why GSE result changes run-by-run ?. Pathways pvalue and NES change each running .
Thank you !