text: user1771: 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
  
  
  user1269: 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.
  
original_text: 1771: <p>I have some data on Copy Number Variation (SNP chip) for a population of samples.</p>
  
  <p>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.</p>
  
  <p>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 <a href="https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/CNV_Pipeline/" rel="noreferrer">GDC</a>?</p>
  
  <p>Should I use (as described in the previously linked page):</p>
  
  <blockquote>
    <p>performing tangent normalization, which subtracts variation that is found in a set of normal samples</p>
  </blockquote>
  
  <p>and do you know of any tool to perform this computation?</p>
  
  <p>The data I have is formatted in this way:</p>
  
  <pre><code>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
  </code></pre>
   1269: <p><a href="http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=216&amp;p=t" rel="nofollow noreferrer">GISTIC</a> does exactly this, and is very possibly the tool used in your link above. </p>
  
  <p>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 <code>.cel</code> files.</p>
  