I have ran copykat on one tumour sample. I was expecting to see aneuploid in the epithelial/tumour cluster and diploid in the remaining cluster. However, I got the opposite result. Please find the clustering below:
I followed the suggestions in issue 18 and limited my analysis to epithelial cells only.
However again I get the error "low confidence in classification" and I see a mix of diploid and aneuploid in the epithelial cells:
Do you know what else I could do to obtain a correct annotation of my clusters?
Good afternoon,
I have ran copykat on one tumour sample. I was expecting to see aneuploid in the epithelial/tumour cluster and diploid in the remaining cluster. However, I got the opposite result. Please find the clustering below:
I do receive the error "low confidence in classification" as described in https://github.com/navinlabcode/copykat/issues/18.
I followed the suggestions in issue 18 and limited my analysis to epithelial cells only. However again I get the error "low confidence in classification" and I see a mix of diploid and aneuploid in the epithelial cells:
Do you know what else I could do to obtain a correct annotation of my clusters?
Thank you very much!