Bioconductor Msmstests

Showing : msmstests • reset

0

votes

8

replies

4.6k

views

proteomics MSnbase MSnSet readMSnSet msmsTests

updated 6.4 years ago by sutturka • 0 • written 8.0 years ago by moldach ▴ 20

4

votes

5

replies

2.9k

views

msnbase msmstests proteomics lc-ms/ms msnID

updated 6.9 years ago by Laurent Gatto 1.6k • written 6.9 years ago by fgol ▴ 10

2

votes

12

replies

2.6k

views

Proteomics msmstests FDR

updated 7.3 years ago by Laurent Gatto 1.6k • written 7.3 years ago by laural710 • 0

3 results • Page 1 of 1

Recent ...

Replies

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…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

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 by 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 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…

Votes

Comment: limpa analysis advice

Answer: When to use edgeR or limma

Awards • All