Problem while computing `cnv_state_post = ...[] about numbat HOT 3 CLOSED

Hi @MigleMi,

Thanks for reporting this. Could you attach your full log.txt? Additionally, did you include the normal cells as input to run_numbat (they shouldn't be included if they are used as reference)?

Thanks,
Teng

from numbat.

Dear Teng,

Thanks for quick response. No I haven't filtered those cells from the count_matrix. I guess then there should not be aggregated counts for aneuploid cells in a reference data as well. Also, what if I don't have a good reference in my data (epithelial cells in this case) but a very few cells that are immune cells? Is it better to find a similar reference, or immune cells will do fine? Thank you again for a cool tool and all the help!
log.txt

from numbat.

Yes, please filter out reference cells from the count_matrix and df_allele. For external reference, you could use ref_hca which ships with the package, which contains epithelial cells and immune cells from the Lung Human Cell Atlas. Generally, variation between cell types is greater than the same cell type between experiments, so you should do fine with an external reference with matched cell type if you don't have good internal references.

from numbat.