Different samples with TCGA Illumina 450K methylationn data between Firebrowse and GDC

[Heery Richard]

Hello,

I was comparing the TCGA samples that are available from GDC and Firebrowse and that have Illumina 450K methylation data available and I noticed that there are a small number of samples that are only available from either GDC or Firebrowse, but not both. In particular, I noticed that from GDC there are occasionally submitters that have multiple tumour samples available (2 or occasionally 3), while this never occurs with Firebrowse. Thus, it seems in these cases that Firebrowse has selected one of these samples to be the representative tumour sample for that submitter. I am wondering if you are able to explain to me a little bit how this was done?

Best,

Richard Heery

Computational Cancer Biology Lab,

IEO, Milan, Italy