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Comment: Combining two proteomics datasets with limpa
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Andrew Pattison
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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
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Gordon Smyth
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Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
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I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
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Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
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Julia Broadbent
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Hi Emily,
Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
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