Showing : Proteomics • reset
1
vote
4
replies
294
views
How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
28 days ago • updated 26 days ago t.b.n.nguyen-9 • 0
0
votes
0
replies
126
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
29 days ago svlachavas ▴ 810
0
votes
5
replies
283
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 8 weeks ago by 1.6k • written 8 weeks ago by • 0
0
votes
1
reply
158
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 8 weeks ago by 1.6k • written 8 weeks ago by • 0
0
votes
2
replies
329
views
Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 9 weeks ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
463
views
biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 6 months ago by 63k • written 6 months ago by • 0
0
votes
0
replies
290
views
Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
6 months ago Laurent Gatto 1.6k
0
votes
0
replies
293
views
Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
7 months ago Laurent Gatto 1.6k
0
votes
0
replies
245
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
7 months ago info ▴ 10
1
vote
3
replies
642
views
Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 8 months ago by 3.8k • written 8 months ago by • 0
1
vote
0
replies
300
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
8 months ago Arend ▴ 10
3
votes
3
replies
714
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 8 months ago by 48k • written 8 months ago by • 0
0
votes
0
replies
278
views
A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
10 months ago Abdullah • 0
0
votes
0
replies
404
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer bioinformatics proteomics genomics phd
10 months ago DKFZ International PhD Program ▴ 10
1
vote
3
replies
606
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
11 months ago proteome_AO • 0
0
votes
5
replies
635
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
325
views
Outliers
Proteomics Proteome
updated 12 months ago by ★ 3.4k • written 12 months ago by • 0
0
votes
0
replies
258
views
Finding DEGs between two different datasets using limma
Proteomics limma proteomi
12 months ago mfaleevs • 0
0
votes
3
replies
642
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 13 months ago by 48k • written 13 months ago by • 0
1
vote
0
replies
427
views
Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
14 months ago Andy Lynch ▴ 120
0
votes
0
replies
439
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
14 months ago qiz218591 • 0
2
votes
5
replies
1.1k
views
proteomics analysis
Proteomics analysis
updated 14 months ago by ▴ 90 • written 14 months ago by • 0
2
votes
1
reply
644
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 16 months ago by 63k • written 16 months ago by • 0
1
vote
2
replies
623
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 15 months ago by 48k • written 16 months ago by • 0
1
vote
0
replies
500
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
17 months ago DKFZ International PhD Program ▴ 10
0
votes
0
replies
517
views
ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
18 months ago ary.lech ▴ 10
0
votes
2
replies
1.3k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 19 months ago by 48k • written 19 months ago by • 0
0
votes
0
replies
542
views
Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
20 months ago Robert Castelo ★ 3.0k
0
votes
1
reply
1.2k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by ▴ 70
0
votes
1
reply
559
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 2.1 years ago by 48k • written 2.1 years ago by • 0
0
votes
5
replies
827
views
In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 2.1 years ago by 48k • written 2.1 years ago by • 0
0
votes
0
replies
610
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.1 years ago barrypraveen • 0
0
votes
1
reply
815
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
1.3k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.2 years ago by • 0
0
votes
4
replies
883
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 5 months ago by 48k • written 2.3 years ago by • 0
4
votes
3
replies
2.7k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 10
0
votes
0
replies
753
views
Limma design multi-level experiment with 3 time points
R proteomics limma
2.5 years ago ellen2270 • 0
6
votes
6
replies
1.3k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 10
0
votes
4
replies
841
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
2.6 years ago rina ▴ 20
0
votes
0
replies
745
views
Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
2.6 years ago Robert Castelo ★ 3.0k
2
votes
1
reply
2.5k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 2.6 years ago by 63k • written 2.6 years ago by ★ 1.5k
0
votes
0
replies
833
views
Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
2.8 years ago Laura • 0
1
vote
2
replies
878
views
calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
2.8 years ago Oliver • 0
0
votes
3
replies
839
views
Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
2.8 years ago Gilad • 0
1
vote
2
replies
840
views
error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 2.8 years ago by ▴ 90 • written 2.8 years ago by • 0
1
vote
0
replies
1.2k
views
News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
2.8 years ago info ▴ 10
5
votes
6
replies
1.2k
views
possible package naming conflict
proteomics
2.8 years ago Tobias ▴ 40
0
votes
1
reply
566
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
updated 7 months ago by 1.6k • written 2.8 years ago by ▴ 20
0
votes
1
reply
864
views
R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 2.8 years ago by ★ 1.3k • written 2.8 years ago by ▴ 20
0
votes
0
replies
709
views
Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
2.9 years ago Robert Ivanek ▴ 730
50 results • Page 1 of 1
Recent ...
Replies
Answer: shinyMethyl - saving the file by Guillaume Devailly ▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Awards • All
Popular Question to Gordon Smyth 48k
Popular Question to James W. MacDonald 63k
Popular Question to nhaus • 0
Popular Question to Bogdan ▴ 660
Popular Question to Michael Love 40k
Locations • All
Salerno, 4 minutes ago
Toulouse, France, 7 minutes ago
Germany/Heidelberg/German Cancer Research Center, 11 minutes ago
WEHI, Melbourne, Australia, 14 minutes ago
Israel, 20 minutes ago
Traffic: 487 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6