Bioconductor Expression

Showing : expression • reset

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3.2k

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expression R filtering limma

3.4 years ago • updated 3.2 years ago mohammedtoufiq91 &utrif; 10

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966

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expression variancePartition edgeR

3.5 years ago Jonathan • 0

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1.8k

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microarray quantile expression R Normalization

updated 4.6 years ago by Konstantinos Yeles &utrif; 90 • written 4.6 years ago by mohammedtoufiq91 &utrif; 10

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1.9k

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GEO expression GEOquery

updated 5.8 years ago by Robert Castelo &starf; 3.4k • written 5.8 years ago by lsbew • 0

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3.6k

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RATs RNA-Seq Isoforms DTU expression

updated 6.6 years ago by fruce_ki &utrif; 20 • written 6.6 years ago by UserAnonyme • 0

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1.2k

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deseq2 genes expression

updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by UserAnonyme • 0

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4.8k

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rpkm scater calcaverage R expression

updated 6.9 years ago by Aaron Lun &starf; 29k • written 6.9 years ago by kushshah &utrif; 10

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2.0k

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variance formula expression

updated 7.1 years ago by mikhael.manurung &utrif; 280 • written 7.1 years ago by rina &utrif; 30

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2.0k

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job sequencing methylation expression Job

11.0 years ago Andy Lynch &utrif; 120

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2.4k

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ebayes expression affymetrix pd.hugene.2.0.st limma

updated 11.1 years ago by Gordon Smyth 53k • written 11.1 years ago by Paulo Nuin &utrif; 200

10 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 &utrif; 760