I have a `RNA-seq` data comparing `responders to chemotherapy` and `non-responders`

I am seeing `CDKN2A (a tumour suppressor)` has been significantly `deleted` in `non-responders` (by `GISTIC`); I then expect that `CDKN2A` be down regulated in non responders `RNA-seq` but I am seeing the swap way, CDKN2A is being up-regulated in non-responders

My confusion is, how a gene is being deleted from chromosome but RNA-seq shows this genes is being up regulated in RNA-seq

Thank you for any information

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