Bioconductor NewWave

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NewWave

updated 2.7 years ago by James W. MacDonald 68k • written 2.7 years ago by SuASNAVASCH • 0

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748

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NewWave

updated 2.4 years ago by Fabricio Almeida-Silva ▴ 40 • written 2.5 years ago by adriana • 0

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NewWave

updated 2.2 years ago by shepherl 4.3k • written 2.2 years ago by 1135296741 • 0

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NewWave

written 2.2 years ago by mario • 0

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NewWave

updated 2.7 years ago by Gordon Smyth 53k • written 2.7 years ago by liujy4 • 0

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mgu74bv2cdf NewWave hgu133a2.db

2.6 years ago roma 0

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mgu74bv2cdf NewWave hgu133a2.db

2.6 years ago roma 0

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NewWave hgu133a2.db

updated 12 weeks ago by MurrayMertz • 0 • written 2.4 years ago by roy23032 • 0

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NewWave

2.4 years ago Kilian • 0

9 results • Page 1 of 1

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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?

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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Scholar to Gordon Smyth 53k

Popular Question to Peter Hickey ▴ 760