Showing : dep • reset
0
votes
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250
views
Warning while loading DEP package
DEP
updated 7 months ago by 4.1k • written 7 months ago by • 0
0
votes
3
replies
691
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 months ago by 51k • written 8 months ago by • 0
1
vote
2
replies
923
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 16 months ago by ▴ 210 • written 17 months ago by ▴ 10
0
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0
replies
667
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
19 months ago aymanreffai • 0
0
votes
1
reply
602
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 20 months ago by ▴ 780 • written 20 months ago by • 0
0
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2
replies
738
views
Error message trying to open downloaded package
error DEP
21 months ago kcpaul168 • 0
0
votes
1
reply
753
views
Issue installing DEP package
DEP
updated 2.3 years ago by 4.1k • written 2.3 years ago by • 0
0
votes
7
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4.3k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.3 years ago by ★ 1.6k • written 2.7 years ago by ▴ 40
0
votes
0
replies
978
views
Introduction to DEP - data imputation
DEP impute
3.2 years ago catherine.li • 0
0
votes
0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
3.3 years ago barrypraveen • 0
0
votes
1
reply
1.0k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
0
votes
1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.3 years ago by • 0 • written 3.3 years ago by • 0
0
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0
replies
2.2k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.4 years ago by • 0
0
votes
0
replies
1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.5 years ago hele7 ▴ 20
1
vote
3
replies
1.6k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
0
votes
2
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1.4k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 27 days ago by • 0 • written 3.6 years ago by ▴ 20
0
votes
3
replies
4.5k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.6 years ago by • 0 • written 3.9 years ago by • 0
1
vote
7
replies
3.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.7 years ago tpm • 0
1
vote
4
replies
1.8k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.7 years ago tpm • 0
0
votes
4
replies
1.3k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.7 years ago rina ▴ 30
3
votes
7
replies
3.9k
views
Error when loading DEP in RStudio
dep
updated 3.8 years ago by ▴ 10 • written 4.2 years ago by ▴ 20
7
votes
2
replies
2.3k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.4 years ago by ▴ 510 • written 4.0 years ago by ▴ 60
0
votes
1
reply
943
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 4.0 years ago by 4.1k • written 4.0 years ago by • 0
3
votes
3
replies
1.2k
views
se does not inherit from class SummarizedExperiment
DEP
4.0 years ago yueli7 ▴ 20
0
votes
0
replies
792
views
Which package I can use?
MSnbase DAPAR DEP
4.0 years ago yueli7 ▴ 20
1
vote
1
reply
1.0k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.1 years ago by ▴ 510 • written 4.1 years ago by ▴ 10
1
vote
6
replies
3.6k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.3 years ago by 1.6k • written 4.3 years ago by • 0
0
votes
1
reply
897
views
Error in generating heatmap
dep
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.9 years ago Rob • 0
0
votes
0
replies
961
views
DEP package - Understanding the results table
dep proteomics logFC
5.1 years ago rina ▴ 30
0
votes
0
replies
1.1k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.2 years ago • updated 5.1 years ago dparrine • 0
0
votes
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.3 years ago tatabox • 0
2
votes
3
replies
1.5k
views
DEP package: error in plot_heatmap
DEP
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by • 0
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by ▴ 510
2
votes
8
replies
2.4k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.3 years ago Wuschel ▴ 10
1
vote
1
reply
972
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 10
3
votes
2
replies
1.8k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.0 years ago • updated 6.8 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.0 years ago by 1.6k • written 7.0 years ago by ▴ 60
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Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
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Answer: Differene between the Wald and LRT test for time-series gene expression data by James W. MacDonald 67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
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Answer: Differene between the Wald and LRT test for time-series gene expression data
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Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
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