I've got a question about copynumber calculation. I used Varscan2 and DNAcopy to call CNV. and got the results as follows:
As we can see that the mean of three logratio valuesis 1.2212. Since the logratio is LOG[(tumor copynumber)/(normal copynumber),2] and we assume that the normal copynumber is 2 copies. If tumor has gained 4 copies than normal sample, the logratio should be LOG[(2+4)/2,2]=LOG(3,2)=1.321928 The result we got(1.2212) is around 1.3219, and if this means that we can predict the tumor sample has gained 4 copies than normal sample.
I wonder if my calculation process is correct. Any suggestion is appreciated.
Thank you for your time.