Showing : DEP • reset
0
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293
views
Warning while loading DEP package
DEP
updated 10 months ago by 4.1k • written 10 months ago by • 0
0
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3
replies
879
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 11 months ago by 52k • written 12 months ago by • 0
1
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2
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1.1k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 19 months ago by ▴ 220 • written 20 months ago by ▴ 10
0
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0
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740
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
22 months ago aymanreffai • 0
0
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1
reply
655
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
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2
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816
views
Error message trying to open downloaded package
error DEP
2.1 years ago • updated 2.0 years ago kcpaul168 • 0
0
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1
reply
835
views
Issue installing DEP package
DEP
updated 2.6 years ago by 4.1k • written 2.6 years ago by • 0
0
votes
7
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4.7k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.6 years ago by ★ 1.6k • written 3.0 years ago by ▴ 40
0
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0
replies
1.1k
views
Introduction to DEP - data imputation
DEP impute
3.5 years ago catherine.li • 0
0
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0
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1.2k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
3.6 years ago barrypraveen • 0
0
votes
1
reply
1.1k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
reply
1.5k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.6 years ago by • 0 • written 3.6 years ago by • 0
0
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0
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2.4k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.6 years ago by • 0
0
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0
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1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.7 years ago hele7 ▴ 20
1
vote
3
replies
1.7k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
0
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2
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1.6k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 4 months ago by • 0 • written 3.9 years ago by ▴ 20
0
votes
3
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4.7k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.9 years ago by • 0 • written 4.1 years ago by • 0
1
vote
7
replies
3.8k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.0 years ago tpm • 0
1
vote
4
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2.0k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.0 years ago tpm • 0
0
votes
4
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1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.0 years ago rina ▴ 30
3
votes
7
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4.0k
views
Error when loading DEP in RStudio
dep
updated 4.1 years ago by ▴ 10 • written 4.5 years ago by ▴ 20
7
votes
2
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2.5k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.7 years ago by ▴ 510 • written 4.2 years ago by ▴ 60
0
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1
reply
1.0k
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 4.3 years ago by 4.1k • written 4.3 years ago by • 0
3
votes
3
replies
1.3k
views
se does not inherit from class SummarizedExperiment
DEP
4.3 years ago yueli7 ▴ 20
0
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0
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847
views
Which package I can use?
MSnbase DAPAR DEP
4.3 years ago yueli7 ▴ 20
1
vote
1
reply
1.1k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.4 years ago by ▴ 510 • written 4.4 years ago by ▴ 10
1
vote
6
replies
3.8k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.6 years ago by 1.6k • written 4.6 years ago by • 0
0
votes
1
reply
971
views
Error in generating heatmap
dep
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
2
replies
2.1k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.1 years ago Rob • 0
0
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0
replies
1.0k
views
DEP package - Understanding the results table
dep proteomics logFC
5.4 years ago rina ▴ 30
0
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0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.4 years ago dparrine • 0
0
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0
replies
1.3k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.5 years ago tatabox • 0
2
votes
3
replies
1.6k
views
DEP package: error in plot_heatmap
DEP
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by • 0
3
votes
3
replies
1.4k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by ▴ 510
2
votes
8
replies
2.6k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.6 years ago Wuschel ▴ 10
1
vote
1
reply
1.1k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
3
votes
2
replies
1.9k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.3 years ago • updated 7.0 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.6k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.3 years ago by 1.6k • written 7.3 years ago by ▴ 60
38 results • Page 1 of 1
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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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