Showing : Proteomics • reset
2
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94
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Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 13 days ago by 59k • written 13 days ago by • 0
0
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0
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34
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
17 days ago Jane • 0
1
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0
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92
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Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
4 weeks ago DKFZ International PhD Program ▴ 10
0
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0
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79
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
10 weeks ago ary.lech ▴ 10
0
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2
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267
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3 months ago by 45k • written 3 months ago by • 0
0
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0
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143
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
3 months ago Robert Castelo ★ 2.9k
0
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1
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329
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limma/voom for protein intensity data
limma proteomics voom
updated 8 months ago by ★ 1.2k • written 8 months ago by ▴ 60
0
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1
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209
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 8 months ago by 45k • written 8 months ago by • 0
0
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5
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337
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 9 months ago by 45k • written 9 months ago by • 0
0
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0
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184
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How to handle the imputation and normalisation?
Proteomics DEP limma
9 months ago barrypraveen • 0
0
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1
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270
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 10 months ago by • 0 • written 10 months ago by • 0
0
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0
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449
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
10 months ago barrypraveen • 0
0
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4
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360
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
11 months ago barrypraveen • 0
4
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3
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973
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 14 months ago by 45k • written 14 months ago by ▴ 10
6
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6
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625
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 14 months ago by 45k • written 14 months ago by ▴ 10
0
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0
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352
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Limma design multi-level experiment with 3 time points
R proteomics limma
14 months ago ellen2270 • 0
0
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4
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377
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
14 months ago rina ▴ 20
0
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0
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370
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
15 months ago Robert Castelo ★ 2.9k
2
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1
reply
1.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 15 months ago by 59k • written 15 months ago by ★ 1.5k
0
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0
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440
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
17 months ago Laura • 0
1
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2
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390
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
17 months ago Oliver • 0
0
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3
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388
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
17 months ago Gilad • 0
1
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2
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397
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error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 17 months ago by ▴ 70 • written 17 months ago by • 0
5
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6
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661
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possible package naming conflict
proteomics
17 months ago Tobias ▴ 30
1
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0
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415
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News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
17 months ago info ▴ 10
0
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0
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225
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
18 months ago yueli7 ▴ 10
0
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1
reply
381
views
R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 18 months ago by ★ 1.0k • written 18 months ago by ▴ 10
0
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0
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377
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Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
18 months ago Robert Ivanek ▴ 730
0
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3
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548
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Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 18 months ago by ▴ 270 • written 18 months ago by • 0
3
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0
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897
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
19 months ago Johannes Rainer ★ 1.9k
2
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0
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393
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Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
20 months ago Johannes Rainer ★ 1.9k
1
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6
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1.3k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 22 months ago by 1.5k • written 22 months ago by • 0
0
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0
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640
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
23 months ago Laurent Gatto 1.5k
0
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0
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225
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How to generate custom MS database using CustomProDB?
r proteomics
2.1 years ago nattzy94 ▴ 20
2
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1
reply
381
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Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
2.2 years ago daniel.magnus.bader ▴ 40
2
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1
reply
369
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
2.2 years ago harelarik ▴ 50
1
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0
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430
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
2.3 years ago Laurent Gatto 1.5k
1
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2
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944
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Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
2.4 years ago Rob • 0
0
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0
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403
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.4 years ago lhuang7 ▴ 50
3
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0
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1.6k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
2.6 years ago • updated 2.4 years ago Gordon Smyth 45k
0
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0
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635
views
News: May Institute Computation and statistics for mass spectrometry and proteomics
conference mass spectrometry proteomics News
2.4 years ago shepherl 3.1k
0
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0
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488
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News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
2.5 years ago info ▴ 10
0
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0
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266
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proteoQC throwing error after running
ProteoQC Proteomics
2.5 years ago laural710 • 0
0
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2
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694
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Total Area Sum Intensity based Normalization for label-free quantitative proteomics
normalization proteomics label-free
2.5 years ago amolares • 0
0
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3
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725
views
Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
0
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0
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298
views
DEP package - Understanding the results table
dep proteomics logFC
2.6 years ago rina ▴ 20
0
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0
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421
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DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
2.7 years ago • updated 2.6 years ago dparrine • 0
2
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0
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1.8k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
2.7 years ago Laurent Gatto 1.5k
0
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0
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329
views
News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
2.7 years ago info ▴ 10
0
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0
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427
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
2.8 years ago tatabox • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10
Dear Basti, thank you so much! Could you please also help me how to arrange samples in the same order in rows (targests2) and columns in (…
Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k
You probably have opened that file in Excel before. Get it again directly from GEO2R, or even better take the R script GEO2R offers and run…
Comment: regression analysis for epic array methylation data using limma by Basti ▴ 280
The columns of your design matrix `var` corresponds to the coefficients that are fitted by limma. If you check your design matrix, you will…
Comment: How to figure out the FC value from Limma by beslinail • 0
I tried to FC column to dbl from chr. But FC colomn is changed by NA genlist_filter <- read_csv(file = "AD_control5.csv") gen…
Comment: WGCNA: correlations module-traits, and module membership-gene significance by annamariabugaj ▴ 10
Hello, sorry for my late response. this is the heatmap: https://drive.google.com/file/d/165fizcsWcA2uzRPVV2cKNPOcqM1d2WfG/view?usp=sharing…
Votes
Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
A: Very low EdgeR Pvalues with very small sample size
A: Very low EdgeR Pvalues with very small sample size
Comment: Question on RNA-Seq single sample data analysis in EdgeR
Answer: Question on RNA-Seq single sample data analysis in EdgeR
Awards • All
Centurion to Basti ▴ 280
Scholar to Robert Castelo ★ 2.9k
Scholar to Gordon Smyth 45k
Popular Question to andrebolerbarros ▴ 10
Scholar to James W. MacDonald 59k
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