I am currently using TCGA-Assembler to download TCGA data. I am interested in the RPKM and RSEM values for each gene. For RSEM i can easily obtain the values per gene (around 20k values per sample). For RPKM, on the other hand, I can only obtain values regarding each exon (around 230k values per sample), not gene. My questions are:
- Does anyone know if TCGA provides RPKM values per gene?
- If not, given that I can map each exon to a gene (TCGA has a mapping for that), is it easy (or even possible?) to obtain the RPKM values per gene, as for the RSEM?
Ps.: I already read the topic Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data.