Bioconductor Expression

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3.1k

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expression R filtering limma

3.2 years ago • updated 3.0 years ago mohammedtoufiq91 ▴ 10

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885

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expression variancePartition edgeR

3.3 years ago Jonathan • 0

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1.7k

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microarray quantile expression R Normalization

updated 4.4 years ago by Konstantinos Yeles ▴ 90 • written 4.4 years ago by mohammedtoufiq91 ▴ 10

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1.8k

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GEO expression GEOquery

updated 5.6 years ago by Robert Castelo ★ 3.4k • written 5.6 years ago by lsbew • 0

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3.2k

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RATs RNA-Seq Isoforms DTU expression

updated 6.5 years ago by fruce_ki ▴ 20 • written 6.5 years ago by UserAnonyme • 0

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1.2k

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deseq2 genes expression

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by UserAnonyme • 0

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4.6k

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rpkm scater calcaverage R expression

updated 6.7 years ago by Aaron Lun ★ 29k • written 6.7 years ago by kushshah ▴ 10

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2.0k

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variance formula expression

updated 6.9 years ago by mikhael.manurung ▴ 280 • written 6.9 years ago by rina ▴ 30

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2.0k

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job sequencing methylation expression Job

10.9 years ago Andy Lynch ▴ 120

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2.4k

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ebayes expression affymetrix pd.hugene.2.0.st limma

updated 10.9 years ago by Gordon Smyth 53k • written 10.9 years ago by Paulo Nuin ▴ 200

10 results • Page 1 of 1

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Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0

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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k

I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…

Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0

Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…

Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k

The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…

Answer: NUPOP usage by shepherl 4.2k

You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…

Votes

C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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