I'm new to NGS data analysis. Recently I am dealing with various types of TCGA cancer data from Genomic browser of UCSC. I found some discrepancies between TCGA data and well-known published data when I performed cancer survival analysis by expression level of certain gene.
I know that the RPKM values of TCGA data have been normalized. I still wonder if we can get more reasonable data when the RPKM value of certain gene are further normalized by that of a reference gene，say, GADPH. Just like what we do when we analysis the results gained from relative quantification in real-time PCR.
Does anyone think it necessary?