data_mrna_seq_v2_rsem.txt

[Wajiha Abdullah]

Hi,

the text file (data_mrna_seq_v2_rsem.txt ) in the TCGA pan-cancer atlas studies on cBioPortal (https://www.cbioportal.org/study/summary?id=blca_tcga_pan_can_atlas_2018) contains RSEM values. Could you please explain exactly what these are? Are the values in the above file normalised? Are they TPM, FPKM?

Kind regards,

Wajiha

[Tim Kuijpers]

Dear Wajiha

RNASeq V2 from TCGA is processed and normalized using RSEM. The RNASeq V2 data in cbioportal corresponds to the rsem.genes.normalized_results file from TCGA. 

You can find some detailed explanation here: https://www.biostars.org/p/106127/ and in the following paper on RSEM.

I  hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal google groups.

Best,

Tim 

Tim Kuijpers

Data Engineer

E timku...@thehyve.nl

W thehyve.nl