Bioconductor MDSplot

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edgeR plotmds differential gene expression MDS mdsplot

updated 7.0 years ago by Gordon Smyth 53k • written 7.0 years ago by ilovesuperheroes1993 • 0

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MDSplot geneexpression insilicomerging

updated 9.7 years ago by James W. MacDonald 68k • written 9.7 years ago by Shamim Sarhadi ▴ 20

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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.…

Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0

In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …

Votes

C: DESeq2 Following RSEM

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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