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Comment: DESEQ2 looking at main effects while controlling for a continuous variable
by
James W. MacDonald
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The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step.
You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable
by
Lennie
•
0
Thank you so much for taking the time and for the detailed explanation!
I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
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
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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
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Gordon Smyth
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I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
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