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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 • 0

Thank you very much James. I corrected the code as you suggested and it fixed the eror. Shajahan

Answer: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde by Aaron Lun ★ 29k

I suspect the real problem is that the knee point is not being identified correctly in your plot. Visually, I would put the knee point some…

Comment: How to use limma to analyze complex temporal RNAseq data by Jinming Cheng • 0

Hi Jiahao, Thanks for more details about your analysis! For my design (`~ 0 + group + time`), confounding factors or interactions were not…

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