RNA seq V2 mRNA calculation information from cBioportal

Question

[david.peeney]

Hi all

I am looking for information on how the RNA seq V2 mRNA values were calculated in cBioportal (data downloaded using R from the Cancer Genomic Data Server (CGDS)). Other questions related to this suggest the following link, but this does not work (https://wiki.nci.nih.gov/display/tcga/rnaseq+version+2).

Thanks,

Dave

[GenoMax]

I am going to suggest that you email GDC support (I assume cBioPortal has not recalculated values that were provided by GDC) at support at nci-gdc.datacommons.io

GDC RNAseq pipeline is described at this link. Data harmonization is described in the links to the right side of the page.

[archana.katta9000]

Hi, I am facing a trouble in downloading cBioportal data, could you please suggest me how to download a data from CGDS. Thank you.

Answer 1

[Kevin Blighe]

This is now in their FAQ: https://docs.cbioportal.org/1.-general/faq#how-is-tcga-rnaseqv2-processed-what-units-are-used

How is TCGA RNASeqV2 processed? What units are used?

RNASeqV2 from TCGA is processed and normalized using RSEM. Specifically, the RNASeq V2 data in cBioPortal corresponds to the rsem.genes.normalized_results file from TCGA. A more detailed explanation of RSEM output can be found here. cBioPortal then calculates z-scores as described above in What are mRNA and microRNA Z-Scores?