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Answer: DESEQ2 looking at main effects while controlling for a continuous variable
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James W. MacDonald
68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa
by
Daniel
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0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Gordon Smyth
52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Devin
▴
10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
•
0
Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…
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Gordon Smyth
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Luca
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Hervé Pagès
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Michael Love
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James W. MacDonald
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