Showing : Proteomics • reset
2
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5
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1.2k
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Dealing with heteroscedascity in limma
limma splines Proteomics
written 7 months ago by • 0
0
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1
reply
420
views
Pathview visualisation not including positive log2 fold changes
pathview Proteomics
updated 9 months ago by 68k • written 9 months ago by • 0
0
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2
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675
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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 11 months ago by ▴ 840
0
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0
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643
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Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
15 months ago Ragnhild • 0
3
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10
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2.0k
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 19 months ago by 68k • written 19 months ago by • 0
0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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0
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1.1k
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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
21 months ago Peter Hickey ▴ 760
0
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1
reply
643
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analysis of overexpressed proteins in metaproteomes
Proteomics ProteoMM ProteomicsWorkflow Proteome
written 2.0 years ago by ▴ 10
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0
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630
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Normalising processed Proteomics data in R
Bioconductor Proteomics
2.0 years ago Joshua • 0
1
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4
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1.7k
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How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
2.3 years ago t.b.n.nguyen-9 • 0
1
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0
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870
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.3 years ago svlachavas ▴ 840
3
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4
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4.1k
views
Protein differential Expression analysis
differential expression proteomics
updated 2.3 years ago by ★ 5.0k • written 7.9 years ago by • 0
0
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1
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1.4k
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
0
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5
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1.5k
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R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
0
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2
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1.6k
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Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 2.4 years ago by • 0 • written 2.5 years ago by • 0
0
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2
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4.0k
views
biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
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0
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1.3k
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
2.8 years ago Laurent Gatto 1.6k
0
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0
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1.2k
views
Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
2.8 years ago Laurent Gatto 1.6k
0
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0
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1.0k
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News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.8 years ago info ▴ 10
0
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1
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1.3k
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
updated 2.8 years ago by 1.6k • written 5.0 years ago by ▴ 20
1
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3
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2.1k
views
Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 2.9 years ago by ★ 4.0k • written 2.9 years ago by • 0
1
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0
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1.1k
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
2.9 years ago Arend ▴ 10
3
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3
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2.5k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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0
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927
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
3.0 years ago Abdullah • 0
0
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0
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1.3k
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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
3.0 years ago DKFZ International PhD Program ▴ 10
1
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3
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1.5k
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
3.1 years ago proteome_AO • 0
0
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5
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1.8k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
0
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0
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966
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Outliers
Proteomics Proteome
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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0
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902
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
3.3 years ago mfaleevs • 0
0
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3
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1.5k
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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 3.3 years ago by 53k • written 3.3 years ago by • 0
1
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0
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1.3k
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
3.4 years ago Andy Lynch ▴ 120
0
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0
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1.3k
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
3.4 years ago qiz218591 • 0
2
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5
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3.0k
views
proteomics analysis
Proteomics analysis
updated 3.4 years ago by ▴ 100 • written 3.4 years ago by • 0
1
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2
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1.7k
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 3.5 years ago by 53k • written 3.6 years ago by ▴ 10
2
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1
reply
1.6k
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Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
1
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0
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1.2k
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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
3.6 years ago DKFZ International PhD Program ▴ 10
0
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0
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1.2k
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
3.7 years ago ary.lech ▴ 10
0
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2
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2.6k
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
0
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0
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1.2k
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
3.9 years ago Robert Castelo ★ 3.4k
0
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1
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3.1k
views
limma/voom for protein intensity data
limma proteomics voom
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 70
0
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1
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1.2k
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
0
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5
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1.8k
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
0
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0
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1.6k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
4.3 years ago barrypraveen • 0
0
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1
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1.8k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
0
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0
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2.7k
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.4 years ago by • 0
0
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4
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2.0k
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 2.7 years ago by 53k • written 4.5 years ago by • 0
5
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6
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6.2k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 22 months ago by • 0 • written 4.7 years ago by ▴ 10
6
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6
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2.5k
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 4.7 years ago by 53k • written 4.7 years ago by ▴ 10
0
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0
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1.3k
views
Limma design multi-level experiment with 3 time points
R proteomics limma
4.7 years ago ellen2270 • 0
0
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4
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1.7k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.8 years ago rina ▴ 30
235 results • Page 1 of 5
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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