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Comment: How to convert .raw data for use in xcms by TikTsossa33ssalpc • 0

It sounds like your mzML conversion has a CV term that XCMS doesn t recognize, which often happens with newer vendor formats or outdated ms…

Comment: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by TikTsossa33ssalpc • 0

To calculate event numbers for boolean combinations in flow cytometry, you should use a logic gating tool or a script that processes popula…

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

Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…

Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

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

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

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Comment: limpa analysis advice

Answer: When to use edgeR or limma

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