I was provided with TCGA-BRCA RNASeq V2 FPKM Tumor-Normal matched data which I intended to perform downstream analysis on. I also have the PAM50 classification based on an older downloaded TCGA-BRCA RNASeq V2 RSEM normalization for the same tumor-normal matched pairs.
Is it correct to use the classification (i.e. Basal, LumA, LumB, Her2-like, Normal) based on a RSEM normalized RNASeq data to perform downstream analysis (e.g. differential analysis, heatmap, etc) but data based on FPKM normalization?
Any help would be helpful in this regard.