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3 hours ago by

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.

Example gene:

Example gene

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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