I am to analyze TCGA data for RNA-Seq of many tumors.
I found that data can be downloaded either from Genomic Data Commons: https://gdc-portal.nci.nih.gov/
or from UCSC Xena:
For what it concerns RNA-Seq data, they do have some differences: for example the former uses FPKM and the latter RSEM; also UCSC Xena are further divided in RNA-Seq v1 and RNA-Seq v2.
What is the relationship between the two data sources? Is there any difference in terms of reliability?