Compute copy number from cases and controls I have some data on Copy Number Variation (SNP chip) for a population of samples.

In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another set (considered as controls) which do not. The cases have not a matched-control. All the controls are taken as a random sample from the population that does not present the disease.

For both cases and controls I have the copy number of some regions. How can I compute the copy number change in cases, such as in GDC?

Should I use (as described in the previously linked page):


  performing tangent normalization, which subtracts variation that is found in a set of normal samples


and do you know of any tool to perform this computation?

The data I have is formatted in this way:

Sample_ID   chrom      start           end  CN
Sample11       19   11991477      12133823   1
Sample11        2   52260564      52431658   1
Sample12        7    5721757       5896192   3
Sample13       10    2269963       2473585   3
GISTIC does exactly this, and is very possibly the tool used in your link above. 

The input files need to be in a different format than what you currently have, but if you're using a SNP6 array, there are guides out there that will tell you how to get the proper files from your .cel files.