Low DESeq2 Sensivity on scRNA Pseudobulk Samples
I'm encountering an unexpected problem when running DESeq2 on pseudobulk scRNAseq datasets. I have three replicates per condition, and although some genes show evident differential expression, DESeq2 gives them extremely high p values. These genes do have low expression, but the size effect is quite reproducible.
All of the standard diagnostic plots look OK (mean - variance fit, heatmaps, PCA).
Any ideas how to increase the sensitivity of the test would are welcome.
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Can you show both the stats of this gene and where it is located on a MA-plot? Is it a low-count gene?