Copy number analysis of X chromosome - TCGA

Question

[kvince.888]

The TCGA has made available files that have gene level amplification/deletion calls. EG. Amplification and deletion calls for every gene [zip] in https://tcga-data.nci.nih.gov/docs/publications/kirc_2013/.

They make the same calls on the X chromosome -- +1, 0 or -1. Is there any sort of correction for the potential of only one copy in males? Or does -1 mean that they no longer have any genomic copy of that gene of interest?

Thanks!

[kvince.888]

There seems to be numerous cases where, in males, there is a "-2" call for certain genes on the X chromosome. How is that possible?