12 days ago
shepherl
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93
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written 4 months ago by
shepherl
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2
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366
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2
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979
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588
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945
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15 months ago • updated 9 months ago
shepherl
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11
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2.8k
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23 months ago • updated 15 months ago
shepherl
4.3k
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4
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2.2k
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3
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1.3k
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3
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18
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5.0k
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2.6 years ago • updated 21 months ago
shepherl
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2
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1.1k
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2.7 years ago • updated 2.6 years ago
Franck RICHARD
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2
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1.6k
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2.8 years ago • updated 2.6 years ago
shepherl
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3
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6
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1.9k
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updated 2.8 years ago by
darrelvanhoy
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0
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written 2.9 years ago by
shepherl
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1.9k
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2.9 years ago
Amanda D. Clark
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written 3.2 years ago by
Robert Castelo
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973
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2
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1.3k
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3.3 years ago • updated 3.2 years ago
shepherl
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1.2k
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3.3 years ago
shepherl
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1.3k
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1.5k
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updated 3.6 years ago by
Gordon Smyth
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written 3.6 years ago by
Jonathan
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4
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1.9k
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3.8 years ago • updated 3.3 years ago
shepherl
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1.1k
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3.8 years ago
shepherl
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4.3 years ago
Guillaume Devailly
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60
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updated 4.3 years ago by
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written 4.3 years ago by
Franck
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1.2k
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4.5 years ago
shepherl
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9
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2.5k
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updated 4.6 years ago by
kayla.interdonato
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160
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written 4.6 years ago by
athief
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20
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1.3k
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4.8 years ago • updated 4.7 years ago
shepherl
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1.4k
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1.1k
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5.8 years ago
shepherl
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1.4k
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2.5k
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updated 10.2 years ago by
Martin Morgan
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written 10.2 years ago by
MarcinKosiński
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1.7k
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updated 10.6 years ago by
Martin Morgan
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written 10.6 years ago by
andrew.j.skelton73
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Replies
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
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0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well.
Cheers,
Andrew
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by
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
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Gordon Smyth
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Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
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Michael Love
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You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
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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