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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

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

You may want to speak with a local statistician, because you don't just want to find the first full rank matrix and run with that if it doe…

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…

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Comment: limpa analysis advice

Answer: When to use edgeR or limma

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