I asked this today on Research Gate, but I'm not receiving any response there... Maybe you folks can help me out.
I am a little disappointed here. After studying a lot of data from these sites, I simply can't find a way to compare the data between them.
My goal is to compare tumor data (cell line or patient samples) and normal tissue data for a particular protein. These sites provide rna-seq and immunohistochemistry (in the case of HPA) data.
From my research, I just can't compare their data for RPKM and FPKM are relative quantitation data and aren't comparable for the most of situations. In addition, CCLE uses RMA!! Man!!!
So, how people make use of the data in these databases? And can I somehow compare the data? Do you know an example of a paper that has done a research using normal x tumor data obtained from these databases and made a valid comparison?
I'm about to lose my mind. Why there isn't a single standard unit for RNA-seq? This is very confusing.
What is the correct way of using GTEx, CCLE and HPA data?