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556 results • Page 1 of 12
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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 by 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 by James W. MacDonald 68k
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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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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Answer: Failure to download resources (MeSHDb) from AnnotationHub
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