Beta values to copy number variation (CNV)

Question

[Tanvir Ahamed]

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!!

Answer 1

[Matt Shirley]

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.

[Tanvir Ahamed]

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