Showing : dep • reset
0
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3
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637
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
7 months ago • updated 6 months ago Shajahan • 0
0
votes
0
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504
views
Warning while loading DEP package
DEP
updated 22 months ago by 4.3k • written 22 months ago by • 0
0
votes
3
replies
1.4k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 23 months ago by 53k • written 24 months ago by • 0
1
vote
2
replies
1.4k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.6 years ago by ▴ 220 • written 2.7 years ago by ▴ 10
0
votes
0
replies
981
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.9 years ago aymanreffai • 0
0
votes
1
reply
1.0k
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error DEP
3.0 years ago kcpaul168 • 0
0
votes
1
reply
1.2k
views
Issue installing DEP package
DEP
updated 3.5 years ago by 4.3k • written 3.5 years ago by • 0
0
votes
7
replies
6.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.5 years ago by ★ 1.6k • written 4.0 years ago by ▴ 40
0
votes
0
replies
1.5k
views
Introduction to DEP - data imputation
DEP impute
4.5 years ago catherine.li • 0
0
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0
replies
1.8k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
4.5 years ago barrypraveen • 0
0
votes
1
reply
1.4k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
votes
1
reply
1.9k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.6 years ago by • 0 • written 4.6 years ago by • 0
0
votes
0
replies
2.9k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.6 years ago by • 0
0
votes
0
replies
1.4k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.7 years ago hele7 ▴ 20
1
vote
3
replies
2.0k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.8 years ago by ▴ 780 • written 4.8 years ago by • 0
0
votes
2
replies
2.3k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 16 months ago by • 0 • written 4.9 years ago by ▴ 20
0
votes
3
replies
5.2k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.9 years ago by • 0 • written 5.1 years ago by • 0
1
vote
7
replies
4.5k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
5.0 years ago • updated 4.9 years ago tpm • 0
1
vote
4
replies
2.4k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
5.0 years ago tpm • 0
0
votes
4
replies
1.8k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
5.0 years ago rina ▴ 30
3
votes
7
replies
4.5k
views
Error when loading DEP in RStudio
dep
updated 5.1 years ago by ▴ 10 • written 5.4 years ago by ▴ 20
7
votes
2
replies
3.2k
views
False discovery rates in DEP
p-value FDR DEP
updated 4.7 years ago by ▴ 510 • written 5.2 years ago by ▴ 60
0
votes
1
reply
1.3k
views
I am using the DEP package example dataset, and I am getting this error on: plot_frequency(data_se)
DEP R Bioconductor Plot
updated 5.3 years ago by 4.3k • written 5.3 years ago by • 0
3
votes
3
replies
1.7k
views
se does not inherit from class SummarizedExperiment
DEP
5.3 years ago yueli7 ▴ 20
0
votes
0
replies
1.1k
views
Which package I can use?
MSnbase DAPAR DEP
5.3 years ago yueli7 ▴ 20
1
vote
1
reply
1.4k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 5.4 years ago by ▴ 510 • written 5.4 years ago by ▴ 10
1
vote
6
replies
4.3k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.6 years ago by 1.6k • written 5.6 years ago by • 0
0
votes
1
reply
1.2k
views
Error in generating heatmap
dep
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
1
vote
2
replies
2.7k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
6.1 years ago Rob • 0
0
votes
0
replies
1.3k
views
DEP package - Understanding the results table
dep proteomics logFC
6.4 years ago rina ▴ 30
0
votes
0
replies
1.7k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.4 years ago dparrine • 0
0
votes
0
replies
1.5k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.5 years ago tatabox • 0
2
votes
3
replies
2.0k
views
DEP package: error in plot_heatmap
DEP
updated 6.5 years ago by ▴ 70 • written 6.6 years ago by • 0
3
votes
3
replies
1.8k
views
Clarification of results tables in DEP
DEP proteomics
updated 6.6 years ago by ▴ 70 • written 6.6 years ago by ▴ 510
2
votes
8
replies
3.2k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.6 years ago Wuschel ▴ 10
1
vote
1
reply
1.3k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 10
3
votes
2
replies
2.6k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
8.2 years ago • updated 8.0 years ago alex.gos90 ▴ 10
2
votes
3
replies
3.1k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 8.2 years ago by 1.6k • written 8.2 years ago by ▴ 60
39 results • Page 1 of 1
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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