dbdimitrov
commented
1 year ago Hi @AltayYuzeir,
Your code looks good.
Might be worth it to check how your cell types are called - i.e. do they have symbols that might be an issue. I assume since the permutations calculation goes through, the next step is a series of joins (where I assume your problem comes up).
You could also lower the number of permutations to check if this would resolve your issue by adding the following parameter:
permutation.params = list(nperms = 100)
Let me know if either helps. Daniel
AltayYuzeir
Hello I have been experiencing some issue with the CellPhoneDB method in liana_wrap() function. It took around 2 hours to come to 100% where it got stuck for more than an hour now and does not move forward with calculating the next method. I will include a screenshot. All other methods were successfully calculated, including external ones, such as call_cellchat. I have done a conversion to mouse, using your vignette, too, if that is relevant. I tried few times, but I always had to terminate the calculation at the end.