I am doing a copy number alteration analysis on liquid biopsies. After using Varscan2 and the R package DNAcopy, I got two very different types of results:
On the left I got what I think it's a clean and clear result, whereas on the right I got a very "dirty" and "noisy" plot, with also a very high residual variance.
Are these samples worth keeping in the analysis? I am fairly new in this kind of analysis, but it is hard for me to trust something like what I got on the right. I was planning to remove those with high residual variance in order to keep the more stable ones, but I am not sure if this is a good practice.
Has any of you experienced something similar? How did you face this issue?
Thank you very much for your time and help!