Bioconductor Multifactorial

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DESeq2 multifactorial nested

updated 2.9 years ago by Basti ▴ 780 • written 2.9 years ago by jd • 0

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DESeq2 LRT multifactorial up/down-reg log2FC

updated 3.2 years ago by James W. MacDonald 68k • written 3.2 years ago by Laia ▴ 10

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DESeq2 time-series timecoursedata timecourse multifactorial

updated 3.2 years ago by Michael Love 43k • written 3.3 years ago by arshad1292 • 0

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Interactions design Multifactorial DESeq2

updated 4.3 years ago by swbarnes2 ★ 1.4k • written 4.3 years ago by Marie • 0

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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…

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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Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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Scholar to Gordon Smyth 53k

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