Hi all!
I want to compare healthy vs cancer gene expression. I have three datasets available: Gtex, TARGET and tcga. All of these datasets are normalized to tpm units. I read about comparing these datasets to each other and there are different opinions: (1) tpm units are enough to compare datasets but you do need to mention that there will always be study variations and (2) use TMM for the tpm units.
What are your opinions? Is it sufficient enough to just compare the datasets with the tpm values?
Thanks!