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ProteomicsWorkflow
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192
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analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 4 months ago by
ary.lech
▴ 10
6
votes
5
replies
6.1k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 7 months ago by
Gordon Smyth
50k • written 2.5 years ago by
David Lyon
▴ 340
0
votes
1
reply
596
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics
RforProteomics
ProteomicsWorkflow
Spectra
MassSpectrometryData
updated 9 months ago by
Laurent Gatto
1.6k • written 9 months ago by
mmvar
• 0
0
votes
5
replies
725
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics
Proteomics
ProteomicsWorkflow
updated 9 months ago by
Laurent Gatto
1.6k • written 9 months ago by
mmvar
• 0
0
votes
2
replies
767
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 9 months ago by
mmvar
• 0 • written 11 months ago by
nkvnambiar
• 0
0
votes
1
reply
826
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow
proteomics
proteinProfiles
updated 14 months ago by
Laurent Gatto
1.6k • written 3.4 years ago by
yueli7
▴ 20
0
votes
3
replies
925
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 20 months ago by
Gordon Smyth
50k • written 20 months ago by
samantha.v.goncalves
• 0
1
vote
2
replies
923
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2
ProteomicsWorkflow
proteomics
updated 22 months ago by
Gordon Smyth
50k • written 24 months ago by
Jane
▴ 10
0
votes
1
reply
740
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles
ProteomicsWorkflow
ProteomicsAnnotationHubData
Proteomics
updated 2.7 years ago by
Gordon Smyth
50k • written 2.7 years ago by
ALOK
• 0
2
votes
1
reply
3.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics
ProteomicsWorkflow
UniProt.ws
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
Dario Strbenac
★ 1.5k
1
vote
0
replies
1.5k
views
News:
Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow
proteomics
Proteome
3.4 years ago
info
▴ 10
0
votes
1
reply
1.0k
views
R package to change protein *.msf file to any readable file
Proteome
ProteomicsWorkflow
proteomics
updated 3.4 years ago by
swbarnes2
★ 1.3k • written 3.4 years ago by
yueli7
▴ 20
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Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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ussarizona
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Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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