again I am struggling with getting TCGAs data and description together. As the title says, it's about CNV data by SNP Arrays.
Reading the wiki page SNP array-based data it says,
Level 3 data describes regions of the genome that seem to have segmental duplications or deletions in the tumor compared to the normal sample for the patient
To me this sound like the relative CNV values have been calculated for paired (Tumor and Control/Normal) samples. But then I am asking myself, why are there normal samples available? In the case of somatic mutations, tumor and matched normal files do not differ (read here), but here they do. Why are there matched normal samples available, if they already have been used for calculations, respectively why do case and control differ?
With all the best,