Showing : DEP • reset
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216
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Warning while loading DEP package
DEP
updated 4 months ago by 4.0k • written 4 months ago by • 0
0
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3
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544
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 months ago by 51k • written 6 months ago by • 0
1
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2
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851
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 14 months ago by ▴ 210 • written 15 months ago by ▴ 10
0
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0
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2.1k
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.2 years ago by • 0
0
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0
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613
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
17 months ago aymanreffai • 0
0
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1
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1.3k
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Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 18 months ago by • 0 • written 3.4 years ago by ▴ 20
0
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1
reply
556
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
0
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2
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687
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Error message trying to open downloaded package
error DEP
19 months ago kcpaul168 • 0
0
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7
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4.0k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.1 years ago by ★ 1.6k • written 2.5 years ago by ▴ 40
0
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1
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708
views
Issue installing DEP package
DEP
updated 2.1 years ago by 4.0k • written 2.1 years ago by • 0
0
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0
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912
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Introduction to DEP - data imputation
DEP impute
3.0 years ago catherine.li • 0
0
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0
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1.1k
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How to handle the imputation and normalisation?
Proteomics DEP limma
3.1 years ago barrypraveen • 0
0
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1
reply
980
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.1 years ago by 67k • written 3.1 years ago by • 0
0
votes
1
reply
1.3k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
7
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2
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2.2k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.2 years ago by ▴ 510 • written 3.8 years ago by ▴ 60
0
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0
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987
views
How to obtain log2 intensity per sample in DEP?
DEP
3.3 years ago hele7 ▴ 20
1
vote
3
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1.5k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
3
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4.4k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.5 years ago by • 0 • written 3.7 years ago by • 0
1
vote
7
replies
3.4k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.5 years ago tpm • 0
1
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4
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1.7k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.5 years ago tpm • 0
0
votes
4
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1.3k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.5 years ago rina ▴ 30
3
votes
7
replies
3.8k
views
Error when loading DEP in RStudio
dep
updated 3.6 years ago by ▴ 10 • written 4.0 years ago by ▴ 20
0
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1
reply
900
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 3.8 years ago by 4.0k • written 3.8 years ago by • 0
3
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3
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1.2k
views
se does not inherit from class SummarizedExperiment
DEP
3.8 years ago yueli7 ▴ 20
0
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0
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753
views
Which package I can use?
MSnbase DAPAR DEP
3.8 years ago yueli7 ▴ 20
1
vote
1
reply
984
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.9 years ago by ▴ 510 • written 3.9 years ago by ▴ 10
1
vote
6
replies
3.5k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.2 years ago by 1.6k • written 4.2 years ago by • 0
0
votes
1
reply
851
views
Error in generating heatmap
dep
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
1
vote
2
replies
1.9k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.7 years ago Rob • 0
0
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0
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907
views
DEP package - Understanding the results table
dep proteomics logFC
4.9 years ago rina ▴ 30
0
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0
replies
1.1k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.0 years ago dparrine • 0
0
votes
0
replies
1.1k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.1 years ago tatabox • 0
2
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3
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1.4k
views
DEP package: error in plot_heatmap
DEP
updated 5.1 years ago by ▴ 70 • written 5.1 years ago by • 0
3
votes
3
replies
1.2k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.1 years ago by ▴ 70 • written 5.2 years ago by ▴ 510
2
votes
8
replies
2.3k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.1 years ago Wuschel ▴ 10
1
vote
1
reply
926
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.4 years ago by 67k • written 5.4 years ago by ▴ 10
3
votes
2
replies
1.7k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.8 years ago • updated 6.6 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.4k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 6.8 years ago by 1.6k • written 6.8 years ago by ▴ 60
38 results • Page 1 of 1
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Answer: Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value by Michael Love 42k
This is covered in the workflow (rnaseqGene). You can filter them, but no they will not negatively affect the multiple testing because o…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Thank you, the strange thing is that I am only getting positive effect sizes. I [see two relevant definitions][1]: - Eff_* : The effect s…
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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