as we know, TCGA offered us a good resource for genomic analysis. Here I have a question, we should subscribe the normal segment score to obtain the somatic value.
However, how to process this approach is quite confusing.
Because the segment region for tumor and normal different quite a lot. So is there any hints for this kind of data?
And another question is that, for CNV data obtained from SNP affy arrays, TCGA offered cnv.seg and nocnv.seg for one sample, so which one should I use? suppose should be cnv.seg, so what's the usage of nocnv.seg file?