Correct for different number of cells and individuals in single cell data analysis
I have scRNAseq from different donors for 4 different conditions. for different condition I have different number of donors and for different condition we have different number of cells. to make the conditions comparable, is there any way to correct for these differences?
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What analysis do you have in mind? Is pseudobulking an option, like, summing counts of cells per gene and cluster/donor/celltype, whatever the setup is?
yes. I am planning to do DGE analysis.
...and does the design allow pseudobulks? That would be preferred, both in terms of statistics, as you do not have the pseudoreplication and inflated power issue of using single-cells, and not the issue of different power due to different cell numbers.