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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?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
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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Answer: Subsetting data verses contrasts [DESeq2]?
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Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
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