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Comment: Getting a large intercept with DESeq2
by
Michael Love
43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette.
And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2
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James W. MacDonald
68k
As a trivial example, consider this:
```
> model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4))))
(Intercept) Tre…
Answer: Getting a large intercept with DESeq2
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James W. MacDonald
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The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
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ATpoint
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There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
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Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
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