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Proteomics
•
reset
2
votes
5
replies
1.1k
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 5 months ago by
Thomas
• 0
0
votes
1
reply
396
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Jessica
• 0
0
votes
2
replies
632
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 9 months ago by
svlachavas
▴ 840
0
votes
0
replies
568
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
13 months ago
Ragnhild
• 0
3
votes
10
replies
1.8k
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Abbey
• 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
james.zhang20
• 0
0
votes
0
replies
933
views
Job:
Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics
JobPosting
SingleCell
Spatial
SpatialExperiment
19 months ago
Peter Hickey
▴ 760
0
votes
1
reply
584
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 22 months ago by
ary.lech
▴ 10
0
votes
0
replies
603
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
23 months ago
Joshua
• 0
1
vote
4
replies
1.5k
views
How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics
proDA
MultipleComparison
2.1 years ago
t.b.n.nguyen-9
• 0
1
vote
0
replies
833
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics
DifferentialRegulation
limma
2.1 years ago
svlachavas
▴ 840
3
votes
4
replies
4.0k
views
Protein differential Expression analysis
differential expression
proteomics
updated 2.2 years ago by
ATpoint
★ 5.0k • written 7.8 years ago by
cardin.julie
• 0
0
votes
1
reply
1.3k
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics
RforProteomics
ProteomicsWorkflow
Spectra
MassSpectrometryData
updated 2.2 years ago by
Laurent Gatto
1.6k • written 2.2 years ago by
mmvar
• 0
0
votes
5
replies
1.4k
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics
Proteomics
ProteomicsWorkflow
updated 2.2 years ago by
Laurent Gatto
1.6k • written 2.2 years ago by
mmvar
• 0
0
votes
2
replies
1.6k
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 2.2 years ago by
mmvar
• 0 • written 2.4 years ago by
nkvnambiar
• 0
0
votes
2
replies
3.9k
views
biomaRt to match UniProt protein IDs with protein names
Proteomics
UniProtKeywords
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
a.a.houfani
• 0
0
votes
0
replies
1.3k
views
Job:
Open position in the CBIO lab: single-cell proteomics
Proteomics
SingleCell
JobPosting
MassSpectrometry
2.6 years ago
Laurent Gatto
1.6k
0
votes
0
replies
1.2k
views
Job:
Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc
proteomics
Spatial
Proteomics
MassSpectrometry
2.6 years ago
Laurent Gatto
1.6k
0
votes
0
replies
958
views
News:
Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics
R
Bioconductor
MassSpectrometry
2.6 years ago
info
▴ 10
0
votes
1
reply
1.2k
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow
proteomics
proteinProfiles
updated 2.6 years ago by
Laurent Gatto
1.6k • written 4.9 years ago by
yueli7
▴ 20
1
vote
3
replies
2.0k
views
Adding ellipse in PCAtools biplot
Biplot
FactoMineR
proteomics
PCAtools
ellipse
updated 2.8 years ago by
Kevin Blighe
★ 4.0k • written 2.8 years ago by
M Tuhin
• 0
1
vote
0
replies
1.0k
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
2.8 years ago
Arend
▴ 10
3
votes
3
replies
2.5k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics
limma
repeated-measures
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Luís C.
• 0
0
votes
0
replies
902
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
2.9 years ago
Abdullah
• 0
0
votes
0
replies
1.3k
views
Job:
PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer
bioinformatics
proteomics
genomics
phd
2.9 years ago
DKFZ International PhD Program
▴ 10
1
vote
3
replies
1.4k
views
Proteomics-time series with repeated measures
Proteomics
limma
repeatedmeasures
TimeSeriesExperiment
3.0 years ago
proteome_AO
• 0
0
votes
5
replies
1.7k
views
Inquiry about suitable package for proteomics study design
Proteomics
design
updated 3.0 years ago by
evocanres
• 0 • written 3.0 years ago by
proteome_AO
• 0
0
votes
0
replies
933
views
Outliers
Proteomics
Proteome
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
bansalheena10
• 0
0
votes
0
replies
860
views
Finding DEGs between two different datasets using limma
Proteomics
limma
proteomi
3.1 years ago
mfaleevs
• 0
0
votes
3
replies
1.5k
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 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
samantha.v.goncalves
• 0
1
vote
0
replies
1.3k
views
Job:
Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics
Proteomics
Cancer
Statistics
Bioinformatics
3.2 years ago
Andy Lynch
▴ 120
0
votes
0
replies
1.2k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
3.2 years ago
qiz218591
• 0
2
votes
5
replies
2.9k
views
proteomics analysis
Proteomics
analysis
updated 3.3 years ago by
jeroen.gilis
▴ 100 • written 3.3 years ago by
Shakiba
• 0
1
vote
2
replies
1.6k
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2
ProteomicsWorkflow
proteomics
updated 3.4 years ago by
Gordon Smyth
53k • written 3.5 years ago by
Jane
▴ 10
2
votes
1
reply
1.6k
views
Extremely low P-values when using Limma on high sample size proteomics data
limma
Proteomics
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
roger.moreno.justicia
• 0
1
vote
0
replies
1.2k
views
Job:
PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd
cancer
genomics
proteomics
bioinformatics
3.5 years ago
DKFZ International PhD Program
▴ 10
0
votes
0
replies
1.2k
views
ProteoMM analysis with two replicates
shotgunproteomics
Proteome
proteomics
Proteomics
ProteoMM
3.6 years ago
ary.lech
▴ 10
0
votes
2
replies
2.6k
views
Limma Differential Analysis on Proteomics data
Proteomics
limma
Limma
DifferentialExpression
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
Mrinal.singh06
• 0
0
votes
0
replies
1.2k
views
Job:
Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics
genomics
proteomics
biologicalchemistry
sequencing
3.7 years ago
Robert Castelo
★ 3.4k
0
votes
1
reply
3.1k
views
limma/voom for protein intensity data
limma
proteomics
voom
updated 4.1 years ago by
ATpoint
★ 5.0k • written 4.1 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.2k
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles
ProteomicsWorkflow
ProteomicsAnnotationHubData
Proteomics
updated 4.1 years ago by
Gordon Smyth
53k • written 4.1 years ago by
ALOK
• 0
0
votes
5
replies
1.7k
views
In need of linear modeling help for differential expression (proteomics)
Proteomics
limma
vsn
updated 4.2 years ago by
Gordon Smyth
53k • written 4.2 years ago by
Chris
• 0
0
votes
0
replies
1.6k
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
4.2 years ago
barrypraveen
• 0
0
votes
1
reply
1.8k
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 4.2 years ago by
bigomics.team
• 0 • written 4.3 years ago by
barrypraveen
• 0
0
votes
0
replies
2.7k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 4.3 years ago by
barrypraveen
• 0
0
votes
4
replies
1.9k
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics
limma
MassSpectrometry
updated 2.5 years ago by
Gordon Smyth
53k • written 4.3 years ago by
barrypraveen
• 0
5
votes
6
replies
6.1k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 21 months ago by
briankleiboeker
• 0 • written 4.6 years ago by
Ridha
▴ 10
6
votes
6
replies
2.4k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics
limma
StatisticalMethod
updated 4.6 years ago by
Gordon Smyth
53k • written 4.6 years ago by
Steve
▴ 10
0
votes
0
replies
1.3k
views
Limma design multi-level experiment with 3 time points
R
proteomics
limma
4.6 years ago
ellen2270
• 0
0
votes
4
replies
1.6k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
4.6 years ago
rina
▴ 30
235 results • Page
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Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
Gabriel
• 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
by
ubjw24
• 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA
by
Rita
• 0
Thank you very much, I appreciate it!
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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