Is there any way to pull TCGA expression data (in both tumor and matched normals) for one single gene? I want to check it in all TCGA sets (I mean, all tumor types), which makes it very heavy download if I'll have to retrieve whole datasets.
I couldn't find such option in GDCquery()
. Also tried to search outside of Bioconductor (cBioPortal for example) with no luck. Any hints?
thanks for the input Kevin! For cBioPortal - I was confused by the fact that in the "Select Molecular Profiles" field it only has choices "Mutation" and "Copy number alterations", nothing like Expression - though it does provide expression data on the output stage. Unfortunately, cBioPortal doesn't have data on matching normal tissue samples for some reasons.
Oh yes, I am not sure that cBioPortal has normal data, but please do check again. It's outside the scope of this forum. If not there, then obtaining multiple datasets via TCGAbiolinks will allow you to re-use these time and time again. To give you an idea, I now have most of the TCGA gene expression datasets re-processed from RSEM estimated counts on my hard-disk.