CLR normalized ADT suitable for pseudobulk analysis

[tdfy]

Hello,

I would like to perform protein differential expression analysis on matched samples comparing two conditions. Similar to your vignette ( below ), only prot. ADT has been CLR ( marg=2 ) normalized. Data integrated on RNA alone.

https://satijalab.org/seurat/articles/de_vignette#:~:text=The%20bulk%20of%20Seurat's%20differential,of%20cells%2C%20specify%20the%20ident.

Can you please advise a suitable approach for this? Could pseudo bulk be employed or FindMarkers()?

Thanks, appreciate your work!