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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
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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If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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