Why object@data.signaling matrix has zero rows?

[CoellEarth]

Dear all,

Thank you so much for inventing such a useful tool!

My teammates and I encountered a problem when we ran the function identifyOverExpressedGenes after setting the subset database to "Secreted Signalling" (which means we ran the code cellchatdb.use <- subsetDB(cellchatdb, search = "Secreted Signalling") beforehand).

After running that function, we received an error message stating: "Error in identifyOverExpressedGenes(cellchat) : Please check object@data.signaling and ensure that you have run subsetData and that the data matrix object@data.signaling looks OK."

Upon checking cellchat@data.signaling, we found the following:

So the core problem seems to be mycellchatobject@data.signaling matrix has zero rows.

The same issue occurred when we chose "Non-protein Signalling".

However, when we selected "Cell-Cell Contact" or "ECM-Receptor" as the search target using the line cellchatdb.use <- subsetDB(cellchatdb, search = " "), no errors occurred, and everything afterwards worked out just fine.

Additionally, when we chose "Cell-Cell Contact" or "ECM-Receptor", the number of highly variable ligand-receptor pairs used for signaling inference was about 400 after running the function identifyOverExpressedInteractions.

Interestingly, if we did not assign a search target and subset the entire database, no error message occurred, and the number of highly variable ligand-receptor pairs used for signaling inference was about 1600 after running the function identifyOverExpressedInteractions. Notably, 1600 is exactly 4 times 400.

Therefore, it seems something went wrong when choosing "Secreted Signalling" and "Non-protein Signalling", but we couldn't figure out why.

Any help or insights on this issue would be greatly appreciated!

Thank you in advance