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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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Proteomics in CellChat #515

Open simonmfr opened 2 years ago

simonmfr commented 2 years ago

Hi, do you have any experience with running proteomics data in Cellchat? Can I just replace RNA expression values with MS-derived protein quantifications, given the correct gene identifiers are present?

Any advice is appreciated! Simon

sqjin commented 1 year ago

@simonmfr If you have protein data, I think that would be better since L-R interactions happen at protein level.

simonmfr commented 1 year ago

Thank you for the response @sqjin!

Is there anything I need to consider when using normalized protein quantification values instead of normalized expression values?