Bioconductor Vsn2

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justvsn vsn Normalization vsn2 Proteomics

3.0 years ago Arend ▴ 10

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vsn vsn2 onestratum

updated 5.0 years ago by Wolfgang Huber ★ 13k • written 5.0 years ago by pros_vs_chur • 0

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vsn vsn2

updated 9.0 years ago by Wolfgang Huber ★ 13k • written 9.0 years ago by Peter Langfelder ★ 3.0k

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limma vsn2

updated 10.3 years ago by Ryan C. Thompson ★ 7.9k • written 10.3 years ago by lukas.burger • 0

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vsn2 limma

updated 10.6 years ago by Wolfgang Huber ★ 13k • written 10.6 years ago by aurelien ▴ 10

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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …

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

Hm, okay, in building a fake model by hand I think I'm realizing the problem: `mouse` and its variants are ideally acting as basically a ra…

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

Ah, this is handy! Hopefully this will help with troubleshooting; at the very least, I can see it being helpful when I try to explain to pe…

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

You may want to look at the coefficients you are trying to estimate with ExploreModelMatrix: https://www.bioconductor.org/packages/relea…

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by emily.wolfrum • 0

Hi Gordon, Thanks for the quick reply. The technical or process blank samples I'm referring to are part of a set of quality control sampl…

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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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