Difference between "gene level copy number" and "gene level copy number scores"

[ysbioinfo]

Hi, thanks for developing such a awesome tool! I download ”gene level copy number“ using TCGAbiolinks, and I supposed there are five values: -2(del),-1(loss),0(diploid),1(gain),2(amp). But when I download the data.type = "gene level copy number scores", there are only 3 values: -1, 0, 1. So I go to GDC and find there are two types of copy number data: "gene level copy number scores" and "gene level copy number", and the latter has 5 values(-2,-1,0,1,2), the former only has 3 values(-1,0,1) I want to know what is the difference between "gene level copy number" and " gene level copy number scores". And is there a way to download "gene level copy number" using TCGAbiolinks?

Thanks!

Yang

[DrZhaoJie]

Hi, I had the same problem with you. And what is the difference between "gene level copy number scores" and " Masker copy number"? Which data type shall we download and analyze. Thank you very much! And my email is [email protected], I'm glad to discuss with you.