Experience with copykat

Question

[Bine]

Good afternoon,

I have recently ran copykat on a tumour sample (kidney cancer). I was expecting to see that my epithelial cells are aneuploid and all the other cells are diploid. However, it was actually showing the opposite but there was a "low confidence in classification" warning.

I was wondering what your experience on copykat is classifying normal/tumour cells. Due to batch effects I understood it is recommended to run it on one sample at a time. I was running it on a sample with around 5000 cells. Is this number too low/high? Are there maybe certain tumours where it is hard to differentiate?

I would appreciate any comments, which might explain my results!

Thank you!