updated 3.4 years ago by
Erik Wright
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written 3.8 years ago by
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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Gordon Smyth
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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?
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Gordon Smyth
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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
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Korneel
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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
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yesquokkan
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Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
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colinmccornack
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FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
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