written 5 months ago by
shepherl
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Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
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0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples.
You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study.
limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
•
0
Thanks for the quick reply!
If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
•
0
Hello, I was also wondering about the same issue. Did you figure it out?
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