I have a question with regards to comparison between RNA seq datasets that have been analyzed using different techniques (in this case FPKM-UQ vs TPM). For reference, the data is cBioportal harvested TCGA data (FPKM-UQ) and GTEx TPMs downloaded from the GTEx portal.
I am not comparing counts between datasets, I am comparing the counts for gene A vs gene X within an individual patient. Basically obtaining a ratio of gene counts. It is this ratio between gene A:gene X that I have been using to compare between datasets.
My question is... Is it reasonable to predict that, in most part, the ratio between gene A and gene X will remain the same (or thereabouts) regardless of whether the counts are FPKM-UQ or TPM?
PS I am aware that it is ideal to re-analyze raw counts using an appropriate between-sample normalization protocol, but this technique allows me to obtain preliminary data from many datasets quickly and identify studies of interest for further in depth analysis.