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4.0 years ago
Frenkiboy
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260
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.
Can you show both the stats of this gene and where it is located on a MA-plot? Is it a low-count gene?