Bioconductor Nested

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866

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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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1.8k

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nested DESeq2

updated 4.0 years ago by Michael Love 43k • written 4.1 years ago by yampolsk • 0

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1.6k

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deseq2 Phyloseq Nested

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by mpuli011 • 0

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1.3k

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deseq2 Paired Nested

updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by julia.chariker ▴ 10

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1.6k

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deseq2 nested de

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by gaio.transposon • 0

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2.0k

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edgeR nested glm glmQLFit

updated 6.8 years ago by Aaron Lun ★ 29k • written 6.8 years ago by jcalis ▴ 10

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3.0k

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edger nested design matrix differential expression

updated 11.0 years ago by Aaron Lun ★ 29k • written 11.0 years ago by Mauve • 0

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2.5k

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edger nested estimatedispersions

11.0 years ago Mauve • 0

8 results • Page 1 of 1

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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…

Votes

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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Popular Question to Peter Hickey ▴ 760