No CellPhoneDB interacions found in this input

[lidd77]

Hello,

I am using CellphoneDB for Xenium 5k data as the input .

cellphonedb method statistical_analysis cell_meta.txt c_counts.txt --counts-data=hgnc_symbol --threads=10

 cell_meta.txt :  two columns（ Cell ， cell_type）
 for cell_type  , it have four types :  
                     type1: 4306 cells  
                     type2: 2398cells  
                     type3: 228 cells  
                     type4: 624 cells
 c_counts.txt  ：4899 genes by 7000 cells  

but I got the error prompt: No CellPhoneDB interacions found in this input .

So CellphoneDB is not work at Xenium 5k data ? or Xenium 5k have fewer gene number ?

Expecting your reply !

[cakirb]

Hello @lidd77,

This is not an error message, it means that CellPhoneDB couldn’t detect any interactions from your dataset.

CellPhoneDB is compatible with Xenium 5k datasets. However, as you mentioned, the relatively smaller number of genes in Xenium 5k datasets can make it more likely to find no detectable interactions.

Additionally, I noticed that you're using CLI commands. Please note that CLI commands have been discontinued after version 5. Instead, you should use CellPhoneDB from Python rather than running commands from the terminal.

If you'd like to use the current version you have, I recommend double-checking that your dataset uses gene symbols rather than ENSG IDs to ensure everything is set up correctly, as your code appears to require gene symbols.

Hope this helps!

Best,
Batu