using raw counts and determening scales in CreasteCasperObject

[anastasija-jakjimovska]

Hi,

I am trying to run CaSpER with raw counts, but I am not observing the expected results. I am seeing a high number of false positive deletions. Has anyone successfully run CaSpER with raw counts? If so, what was your experience?

Additionally, is there a recommended approach for determining the optimal thresholds for cnv.scale and loh.scale based on dataset characteristics? Any guidance on parameter tuning would be greatly appreciated!

Thanks in advance for your help.