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The basemean is described as the "mean of normalized counts of all samples". My question is, how would we interpret differences in basemean between genes, pertaining to reliability and such? For example, if two genes that have similar p-values and l2fchanges, but one has a much higher basemean, would that gene's data be more dependable?

Sorry if this is a trivial question!

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I could write a long story about this but actually I will just link this excellent resource from HBCtraining which dissects the individual steps DESeq2 does, starting from normalization over dispersion estimation (this is where the baseMean comes into play) over model fitting and testing. I think it will clarify the role of the baseMean in DESeq2.

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