Showing : dep • reset
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 10
3
votes
7
replies
3.5k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
1
vote
7
replies
3.1k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.1 years ago tpm • 0
0
votes
7
replies
3.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 20 months ago by ★ 1.6k • written 2.1 years ago by ▴ 40
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.7 years ago by 1.6k • written 3.7 years ago by • 0
0
votes
4
replies
1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.1 years ago rina ▴ 30
1
vote
4
replies
1.5k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.1 years ago tpm • 0
0
votes
3
replies
264
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
3
replies
2.1k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 6.4 years ago by 1.6k • written 6.4 years ago by ▴ 60
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.7 years ago by ▴ 70 • written 4.8 years ago by ▴ 490
2
votes
3
replies
1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
3
votes
3
replies
954
views
se does not inherit from class SummarizedExperiment
DEP
3.4 years ago yueli7 ▴ 20
0
votes
3
replies
4.1k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.1 years ago by • 0 • written 3.3 years ago by • 0
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by ▴ 770 • written 3.0 years ago by • 0
1
vote
2
replies
1.7k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
1
vote
2
replies
638
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 9 months ago by ▴ 190 • written 10 months ago by ▴ 10
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.4 years ago • updated 6.2 years ago alex.gos90 ▴ 10
7
votes
2
replies
1.9k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.8 years ago by ▴ 490 • written 3.4 years ago by ▴ 60
0
votes
2
replies
531
views
Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
1
vote
1
reply
842
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.5 years ago by ▴ 490 • written 3.5 years ago by ▴ 10
0
votes
1
reply
776
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 3.4 years ago by 3.8k • written 3.4 years ago by • 0
0
votes
1
reply
417
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 13 months ago by ▴ 770 • written 13 months ago by • 0
0
votes
1
reply
573
views
Issue installing DEP package
DEP
updated 20 months ago by 3.8k • written 20 months ago by • 0
1
vote
1
reply
783
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by • 0 • written 3.0 years ago by ▴ 20
0
votes
1
reply
831
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.7 years ago by • 0 • written 2.8 years ago by • 0
0
votes
1
reply
716
views
Error in generating heatmap
dep
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
0
votes
0
replies
773
views
Introduction to DEP - data imputation
DEP impute
2.6 years ago catherine.li • 0
0
votes
0
replies
1.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
votes
0
replies
637
views
Which package I can use?
MSnbase DAPAR DEP
3.4 years ago yueli7 ▴ 20
0
votes
0
replies
887
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
0
replies
984
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
0
votes
0
replies
778
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
0
votes
0
replies
26
views
Warning while loading DEP package
DEP
updated 17 hours ago by 3.8k • written 18 hours ago by • 0
0
votes
0
replies
929
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago • updated 4.5 years ago dparrine • 0
0
votes
0
replies
791
views
DEP package - Understanding the results table
dep proteomics logFC
4.5 years ago rina ▴ 30
0
votes
0
replies
467
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
38 results • Page 1 of 1
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Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
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