Showing : proteomics • reset
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 4 hours ago by 65k • written 5 hours ago by • 0
0
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3
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146
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
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227
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
9 weeks ago Peter Hickey ▴ 740
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1
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205
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analysis of overexpressed proteins in metaproteomes
Proteomics ProteoMM ProteomicsWorkflow Proteome
written 5 months ago by ▴ 10
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246
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Normalising processed Proteomics data in R
Bioconductor Proteomics
5 months ago Joshua • 0
1
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4
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754
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How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
8 months ago t.b.n.nguyen-9 • 0
1
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0
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456
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
8 months ago svlachavas ▴ 830
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5
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747
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R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 9 months ago by 1.6k • written 9 months ago by • 0
0
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1
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616
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R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 9 months ago by 1.6k • written 9 months ago by • 0
0
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2
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802
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Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 9 months ago by • 0 • written 11 months ago by • 0
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2
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1.3k
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biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 14 months ago by 65k • written 14 months ago by • 0
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0
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651
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
14 months ago Laurent Gatto 1.6k
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642
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Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
14 months ago Laurent Gatto 1.6k
0
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519
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News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
14 months ago info ▴ 10
1
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3
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1.2k
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Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 15 months ago by ★ 3.9k • written 15 months ago by • 0
1
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0
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578
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
16 months ago Arend ▴ 10
3
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3
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1.3k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 16 months ago by 50k • written 16 months ago by • 0
0
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0
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509
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
17 months ago Abdullah • 0
0
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0
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712
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Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer bioinformatics proteomics genomics phd
17 months ago DKFZ International PhD Program ▴ 10
1
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3
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918
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Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
18 months ago proteome_AO • 0
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5
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1.0k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 18 months ago by • 0 • written 18 months ago by • 0
0
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0
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564
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Outliers
Proteomics Proteome
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
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482
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
20 months ago mfaleevs • 0
0
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3
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936
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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 50k • written 21 months ago by • 0
1
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0
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764
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
21 months ago Andy Lynch ▴ 120
0
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0
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731
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
2
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5
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1.8k
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proteomics analysis
Proteomics analysis
updated 22 months ago by ▴ 90 • written 22 months ago by • 0
2
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1
reply
1.0k
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Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 24 months ago by 65k • written 24 months ago by • 0
1
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2
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934
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 23 months ago by 50k • written 2.0 years ago by ▴ 10
1
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0
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741
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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
2.0 years ago DKFZ International PhD Program ▴ 10
0
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0
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755
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
2.2 years ago ary.lech ▴ 10
0
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2
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1.8k
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
0
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0
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765
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
2.3 years ago Robert Castelo ★ 3.3k
0
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1
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1.8k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 70
0
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1
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752
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 2.7 years ago by 50k • written 2.7 years ago by • 0
0
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5
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1.1k
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 2.7 years ago by 50k • written 2.7 years ago by • 0
0
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0
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909
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How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
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1
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1.1k
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
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0
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1.8k
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
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4
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1.2k
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 13 months ago by 50k • written 2.9 years ago by • 0
5
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6
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3.8k
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
0
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0
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945
views
Limma design multi-level experiment with 3 time points
R proteomics limma
3.2 years ago ellen2270 • 0
6
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6
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1.7k
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.1 years ago by 50k • written 3.2 years ago by ▴ 10
0
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4
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1.1k
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.2 years ago rina ▴ 30
0
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0
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958
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
3.2 years ago Robert Castelo ★ 3.3k
2
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1
reply
3.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 3.3 years ago by 65k • written 3.3 years ago by ★ 1.5k
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1.1k
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
3.4 years ago Laura • 0
1
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2
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1.2k
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
3.4 years ago Oliver • 0
0
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3
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1.1k
views
Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
3.4 years ago Gilad • 0
1
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2
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1.1k
views
error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 3.4 years ago by ▴ 90 • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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