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ProteomicsWorkflow
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Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
5 weeks ago • updated 25 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 16 months ago by
Laurent Gatto
1.6k • written 16 months ago by
Jane_Huang
• 0
0
votes
1
reply
693
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 2.2 years ago by
ary.lech
▴ 10
6
votes
5
replies
14k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 2.4 years ago by
Gordon Smyth
53k • written 4.3 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 2.6 years ago by
Laurent Gatto
1.6k • written 2.6 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 2.6 years ago by
Laurent Gatto
1.6k • written 2.6 years ago by
mmvar
• 0
0
votes
2
replies
1.7k
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 2.6 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 3.0 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 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
samantha.v.goncalves
• 0
1
vote
2
replies
1.9k
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2
ProteomicsWorkflow
proteomics
updated 3.7 years ago by
Gordon Smyth
53k • written 3.8 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 4.5 years ago by
Gordon Smyth
53k • written 4.5 years ago by
ALOK
• 0
2
votes
1
reply
5.4k
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
2.2k
views
News:
Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow
proteomics
Proteome
5.2 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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Answer: Unable to create venndiagram using VennDiagram 1.5.1 package
by
kesha
• 0
<a href=https://vavadacasinox.com/>vavadacasinox.com</a>
Comment: How to convert .raw data for use in xcms
by
a2a2asawhaa
• 0
try converting your files to the older mzXML format, which remains highly stable for XCMS. While waiting for large datasets to process, you…
Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
• 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Votes
A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
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