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How do I convert the Copy Number (CN) file into useful information such as HOMDEL and AMP?

This is an already normalized file with pseudo count + 1. In this file there are values from 0 to 1 for each cancer cell line, in wide format.

I have already looked at the forum post about the file, but it's not helpful for me.

This is what the file looks like:

,DDX11L1 (100287102),WASH7P (653635),FAM138A (645520),OR4F5 (79501)

Thank you for your help


1 Answer 1


I'm not familiar with this file structure, but have you looked at the forum post about relative copy number linked to in the FAQ?

Since we do not have matched normals, the output is a “copy ratio” or relative copy number. It is relative to the rest of the genome for that cell line. E.g. if the cell line is tetraploid we would not be able to see it from the relative copy number. These values are reported as log2(relative CN + 1) in the portal.

  • 1
    $\begingroup$ Yes I checked but I still have the same doubts $\endgroup$
    – flavinsky
    Jan 24, 2022 at 10:50

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