Cross TCGA Pan Cancer Atlas study expression analysis in private cBioPortal

[Shayna Simonstein]

Hello, 

In the public cBioPortal, if I select multiple TCGA PanCancer Atlas (2018) studies, I can compare mRNA expression and protein levels across the studies. I added these same studies to a privately deployed cBioPortal, but this feature is not available. If I select multiple TCGA PanCancer Atlas studies, I am no longer able to view expression. I downloaded the studies from the cbioportal website (https://www.cbioportal.org/datasets), so they should have the same meta data information. I was wondering if there is a way to enable cross study expression analysis in a privately deployed panel for these tcga pan cancer studies?

Thank you,

Shayna

[Tali Mazor]

Hi Shayna,

By default, cross-study expression analysis is not allowed, but there is a portal property you can set to enable this. 

For the portal, you'll want to set this property: enable_cross_study_expression (documented here)

It can be set to either:
- True / False
- A dynamic JavaScript function string for advanced rules. For example to enable cross-study expression for the TCGA PanCancer Atlas studies:

         enable_cross_study_expression: '(studies) => studies.filter(s => /pan_can_atlas/.test(s.studyId) === false).length === 0'

-Tali

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[Shayna Simonstein]

Thanks, Tali!!