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Answer: Difference between logFC in limma-voom and weighted limma-voom
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Gordon Smyth
52k
No, your formula is not correct, for several reasons. voom is always a weighted method, whether it includes sample weights or not. The samp…
Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde
by
Aaron Lun
★
29k
It's all heuristic anyway, so it's not surprising to give or take a few thousand cells. I suspect you'd get that much variation if you fidd…
Comment: How to use limma to analyze complex temporal RNAseq data
by
Jiahao Tian
•
0
Thank you so much! I would compare every two groups separately.
Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde
by
Peter Hickey
▴
760
Ah, I'd forgotten about how the knee comes into the calculation.
Your proposal does do a better job at finding the knee and the subsequent…
Comment: DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not a
by
Shajahan
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0
Thank you very much James. I corrected the code as you suggested and it fixed the eror.
Shajahan
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