cBioPortal Z-score: value difference between download and web Portal

Question

[faswad]

I am using the cBioPortal R library (cgdsr) to download data from cBioPortal. I am currently focused on the z-score mRNA expression data. For a given sample and gene combination, the z-score that is downloaded does not match the one on the web version of cBioPortal. Could someone shed light on why there is a difference?

Thank you.

[Kevin Blighe]

Are you sure that you are accessing the exact same study in both R and on the cBioPortal website? Some of the TCGA studies are 'provisional' and have different numbers of samples from the published versions.