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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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The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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Hi,
I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation.
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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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