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Beta values to copy number variation (CNV)

For 450k data,

  1. one can get CNV form .idat file
  2. one can get M values or beta values .idat file

But I am interested to get CNV form the beta values (GSE50025-GPL13938_series_matrix.txt), if this is possible .

Any help will be appreciated.

Thanks!!

methylation
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updated by Ram Ram • written by Tanvir Ahamed Tanvir Ahamed

1 answer

You will not be able to get CNV state from beta values - for that you'll need to get the idat files with probe intensities and use something like Epicopy to normalize and segment on the intensities.

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updated by Ram Ram • written by Matt Shirley Matt Shirley

Thanks Matt!! I was wondering if that is somehow possible!! :( But no hope.

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updated by Ram Ram • written by Tanvir Ahamed Tanvir Ahamed

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