Open GabyBG opened 8 months ago
Hi, it seems that the genes defined in the annotations
variable are not found in your adata
object, this causes the error that you're seeing. We'll implement a more verbose warning in the next patch, thanks for raising this issue.
To solve this, ensure that the gene names in adata.var_names
match your annotations. Cytopus uses capital letters only for genes, without spaces or special characters (for example STAT6
, RAB1A
, ..). Please let me know if that helped.
Hi. Even after doing as suggested it threw the same error at the end of the training. I then flattened the dictionary such that it has only one level and the training succeeded. However, I guess this is not the right way to do it as you want a hierarchy of cell type -> processes. (correct me if I am wrong)
Hello, I am trying to run spectra using cell type labels:
It finishes the process, but gives the following error: