Open Sophia409 opened 1 month ago
Did you carefully read the messages that were returned?
This is the key remark:
There are ties in the preranked stats (80.9% of the list).
In other words, 81% of your input data has an identical ranking metric! Why? This cannot be correct...
Anyway, this results in behavior reported before: https://github.com/ctlab/fgsea/issues/151
Hello, I am encountering an issue while using the gseKEGG function from the clusterProfiler package for GSEA enrichment analysis. I have provided a gene list containing just over 3000 genes, but the function has been running for two hours without completing. I manually stopped the process and attempted to modify the function parameters, but after several tries, the function still hangs. Here are the details of my setup: clusterProfiler version: 4.12.0 (latest version) I would appreciate any insights into why this might be happening and how I can resolve this issue. Thank you for your help! Best regards,