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ProteomicsWorkflow
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0
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2
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263
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Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
16 days ago • updated 2 days ago
Andrew Pattison
• 0
2
votes
4
replies
1.1k
views
Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentifications?
ProteomicsWorkflow
PSMatch
Spectra
RforProteomics
updated 15 months ago by
Laurent Gatto
1.6k • written 16 months ago by
Jane_Huang
• 0
0
votes
1
reply
680
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 2.2 years ago by
ary.lech
▴ 10
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 2.4 years ago by
Gordon Smyth
53k • written 4.2 years ago by
David Lyon
▴ 340
0
votes
1
reply
1.5k
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics
RforProteomics
ProteomicsWorkflow
Spectra
MassSpectrometryData
updated 2.5 years ago by
Laurent Gatto
1.6k • written 2.5 years ago by
mmvar
• 0
0
votes
5
replies
1.6k
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics
Proteomics
ProteomicsWorkflow
updated 2.5 years ago by
Laurent Gatto
1.6k • written 2.5 years ago by
mmvar
• 0
0
votes
2
replies
1.7k
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 2.5 years ago by
mmvar
• 0 • written 2.7 years ago by
nkvnambiar
• 0
0
votes
1
reply
1.3k
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow
proteomics
proteinProfiles
updated 2.9 years ago by
Laurent Gatto
1.6k • written 5.2 years ago by
yueli7
▴ 20
0
votes
3
replies
1.6k
views
Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates not of…
limma
Proteomics
ProteomicsWorkflow
updated 3.4 years ago by
Gordon Smyth
53k • written 3.5 years ago by
samantha.v.goncalves
• 0
1
vote
2
replies
1.8k
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2
ProteomicsWorkflow
proteomics
updated 3.6 years ago by
Gordon Smyth
53k • written 3.7 years ago by
Jane
▴ 10
0
votes
1
reply
1.2k
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles
ProteomicsWorkflow
ProteomicsAnnotationHubData
Proteomics
updated 4.4 years ago by
Gordon Smyth
53k • written 4.4 years ago by
ALOK
• 0
2
votes
1
reply
5.3k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics
ProteomicsWorkflow
UniProt.ws
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
Dario Strbenac
★ 1.6k
1
vote
0
replies
2.1k
views
News:
Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow
proteomics
Proteome
5.1 years ago
info
▴ 10
0
votes
1
reply
1.5k
views
R package to change protein *.msf file to any readable file
Proteome
ProteomicsWorkflow
proteomics
updated 5.2 years ago by
swbarnes2
★ 1.4k • written 5.2 years ago by
yueli7
▴ 20
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Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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