I had downloaded TCGA RNA-seq data using tcgabiolinks package. In the data I see that there few samples with same barcode. Which sample should I prefer?
From TCGA barcode I see that plate and center are different but the sample ID (TCGA-A6-2684-01) is same. Which one should I prefer for the analysis? Do I need to keep both the samples? When I consider sample ID it will be duplicate samples.