I have a list of 500 genes of my interest in a certain cancer type.
I would like to know if these genes are significantly amplified/loss or not respectively.
Is there any way to collect the CNV analysis result (such as q-value) for the 500 genes from TCGA CN portal (http://www.broadinstitute.org/tcga/home) ?
I read FAQ and help in TCGA CN portal, but I still don't know the way.
Also, I sent this question to the support e-mail address (tcga-help[at]broadinstitute.org), but it was rejected by the server.
I also knows there is GDAC Firehose pipeline though, I would like to use the TCGA CN portal pipeline.