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Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
It looks to me that everything is working ok and limpa has done the right thing. You data has a lot of missing values, with the proportion …
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
by
Gordon Smyth
53k
Yes, you could probably use the voom sample weights for an analysis of the GSVA scores for the same data, although I have never tried it.
…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Erik Wright
▴
160
You are correct. Thank you for noticing some of this 'pollution' with "_2" suffixes was unnecessary.
I posted an updated SILVA classifier …
Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
•
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…
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