Hello, I have 136 cell surface protein label data in my scRNA seq data. I normalized the protein data with "CLR", I have 8 samples in each treatment. I understand I need do pseudobulk analysis before the differential expression of Gene analysis. My questions is, for the small number of Protein, should I still need to do the pseudobulk analysis before I do the differential expression on the protein? I tried pseudobulk analysis before I do the protein differential analysis, no significant protein was found, I want to know if I can do 136 protein differential analysis without pseudobulk analysis? is it acceptable in statistics? I really appreciate if any professional suggestions.

Best, Lei

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