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Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons
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If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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