GSEA with single cell seq data
I have 130 single cell RNA seq TPMs (all normalized to 1E6 reads). ~30 can be clearly distinguished by expression of a known marker, and I wanted to test for enrichment of other specific genes within this dataset. The single cell data itself is interesting, but the expression of this known marker clearly divides them into their own group and classifies them as a specific cell type. Is there any reason I couldn't just pool the 2 populations and compare enrichment between them?
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