Bioconductor Entrez

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2.6k

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gage annotationdbi entrez ensembl

8.0 years ago colaneri ▴ 30

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3.3k

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annotation entrez gene ids software error

updated 6.8 years ago by Gordon Smyth 53k • written 6.8 years ago by Raito92 ▴ 60

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2.4k

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conversion symbol entrez

updated 10.4 years ago by James W. MacDonald 68k • written 10.4 years ago by dalloliogm ▴ 50

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2.2k

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ensembl entrez biomart org.hs.eg.db

updated 7.2 years ago by James W. MacDonald 68k • written 7.2 years ago by bettina.budeus • 0

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6.4k

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microarray limma kegg ENTREZ enrichment analysis

updated 6.0 years ago by Gordon Smyth 53k • written 6.0 years ago by omarrafiqued ▴ 50

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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