saeyslab
How to choose the best ligand to continue analysis with the potential ligand?
Dear nichenetr team, I did run nichnetr on my single cell dataset. I do have problem choosing the best potential ligand. I have observed discrepancies in my analysis results, particularly with regards to the relationship between ligand expression levels and log fold change (LFC).
Specifically, I noticed instances where a ligand exhibits low expression levels but a high LFC, and conversely, where a ligand shows high expression levels but a negative LFC (like LAMA2 in the below plot). Could you please provide insight into the interpretation of these findings? I am unsure if this discrepancy reflects an error in my approach or if there is a specific biological interpretation behind these observations.
Moreover, I was wondering what is the best ligand activity AUPR as if I compare with other ligands the range might not be good enough overall.
Thank you very much for your help on this matter. Paria
