I was going to compare gene expression in primary tumor and normal control.
So I downloaded PAN cancer data from xena.USCS.edu (https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/PANCAN_clinicalMatrix
for clinical matrix and
https://toil.xenahubs.net/download/tcga_RSEM_gene_fpkm for gene expression TOIL Gene RSEM fpkm dataset.
Then I selected patient that have matched normal and primary tumor sample types, and I found that for each gene, fpm from normal and primary tumor are JUST THE SAME!
I wonder what's wrong with this.
Is there anybody helping me? Thanks in advance!