Showing : DEP • reset
0
votes
0
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117
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Warning while loading DEP package
DEP
updated 15 days ago by 3.9k • written 15 days ago by • 0
0
votes
3
replies
284
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
1
vote
2
replies
663
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 9 months ago by ▴ 200 • written 10 months ago by ▴ 10
0
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0
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484
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
votes
1
reply
433
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 13 months ago by ▴ 780 • written 13 months ago by • 0
0
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2
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549
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Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
0
votes
1
reply
591
views
Issue installing DEP package
DEP
updated 21 months ago by 3.9k • written 21 months ago by • 0
0
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7
replies
3.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 21 months ago by ★ 1.6k • written 2.2 years ago by ▴ 40
0
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0
replies
800
views
Introduction to DEP - data imputation
DEP impute
2.7 years ago catherine.li • 0
0
votes
0
replies
904
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How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
1
reply
849
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
0
votes
0
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1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
votes
0
replies
802
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
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 3.1 years ago by ▴ 20
0
votes
3
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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
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
1
vote
4
replies
1.6k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.2 years ago • updated 3.1 years ago tpm • 0
0
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4
replies
1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.2 years ago rina ▴ 30
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.3 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.9 years ago by ▴ 510 • written 3.4 years ago by ▴ 60
0
votes
1
reply
794
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 3.5 years ago by 3.9k • written 3.5 years ago by • 0
3
votes
3
replies
974
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 20
0
votes
0
replies
651
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
1
vote
1
reply
856
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.6 years ago by ▴ 510 • written 3.6 years ago by ▴ 10
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.8 years ago by 1.6k • written 3.8 years ago by • 0
0
votes
1
reply
728
views
Error in generating heatmap
dep
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
2
replies
1.8k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
0
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0
replies
800
views
DEP package - Understanding the results table
dep proteomics logFC
4.6 years ago rina ▴ 30
0
votes
0
replies
942
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago dparrine • 0
0
votes
0
replies
1000
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
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
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by ▴ 510
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 years ago Wuschel ▴ 10
1
vote
1
reply
795
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.1 years ago by 65k • written 5.1 years 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
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
38 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
You seem to have the misunderstanding that you can change the design matrix but keep all the other code unchanged. The contrasts are comput…
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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