Dear Gordon!

sorry for being unclear. A and B are two distinct cell-surface proteins,
whereas C1 and C2 are two different cell types, that were exposed to those
treatments. Therefore I'd like to extract DEGs between cells with cell type
C1 and expressing protein A (C1.A) and the rest of the cell populations
(i.e. the combinations C1.B, C2.A and C2.B). Additionally, I have to
control for the fact that in most instances cells were derived from the
same donor. Do you see a straight forward way of getting the afore
mentioned DEGs?

Kind regards,

Mitja

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