Bioconductor Forum

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limpa MassSpectrometry MassSpectrometryData

updated 9 hours ago by ATpoint ★ 5.0k • written 2 days ago by DN • 0

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DESeq2

updated 21 hours ago by Gordon Smyth 53k • written 3 days ago by chp265 • 0

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Bioconductor CellChat

updated 13 hours ago by LillianaVolkman99 • 0 • written 10 days ago by Omer • 0

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ChemmineOB Install

updated 12 hours ago by Jeremy • 0 • written 19 months ago by jrbald04 • 0

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Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k

Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …

Comment: chemmineOB install help by Jeremy • 0

I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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