I have obtained TCGA RSEM data for STAD using FireBrowse, I found that there are two types of files for RSEM RNASeqV2 1) illuminahiseqrnaseqv2-RSEMgenes (MD5) 2) illuminahiseqrnaseqv2-RSEMgenes_normalized (MD5)
I think 1) illuminahiseq_rnaseqv2-RSEM_genes file is the most suitable for subsequent analysis with DESeq2 imported through tximport.
There are 3 columns associated with each samples in the 1) illuminahiseqrnaseqv2-RSEMgenes file: "raw count", "scaled estimate" and "transcript id". I feel "raw count" (in reality probably it is estimated counts because data not in integer format) column will be more appropriate for DESeq2 analysis imported via tximport.
If anyone please confirm me, whether I am correct or not.