Showing : DEP • reset
2
votes
8
replies
3.1k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.5 years ago Wuschel ▴ 10
3
votes
7
replies
4.5k
views
Error when loading DEP in RStudio
dep
updated 5.0 years ago by ▴ 10 • written 5.3 years ago by ▴ 20
1
vote
7
replies
4.4k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.9 years ago • updated 4.8 years ago tpm • 0
0
votes
7
replies
6.1k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.4 years ago by ★ 1.6k • written 3.9 years ago by ▴ 40
1
vote
6
replies
4.3k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.5 years ago by 1.6k • written 5.5 years ago by • 0
0
votes
4
replies
1.8k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.9 years ago rina ▴ 30
1
vote
4
replies
2.3k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.9 years ago tpm • 0
0
votes
3
replies
589
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
5 months ago Shajahan • 0
2
votes
3
replies
3.0k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 8.1 years ago by 1.6k • written 8.1 years ago by ▴ 60
3
votes
3
replies
1.7k
views
Clarification of results tables in DEP
DEP proteomics
updated 6.5 years ago by ▴ 70 • written 6.5 years ago by ▴ 510
2
votes
3
replies
1.9k
views
DEP package: error in plot_heatmap
DEP
updated 6.4 years ago by ▴ 70 • written 6.5 years ago by • 0
3
votes
3
replies
1.7k
views
se does not inherit from class SummarizedExperiment
DEP
5.2 years ago yueli7 ▴ 20
0
votes
3
replies
5.1k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.8 years ago by • 0 • written 5.0 years ago by • 0
1
vote
3
replies
2.0k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.7 years ago by ▴ 780 • written 4.7 years ago by • 0
0
votes
3
replies
1.3k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error DEP
2.9 years ago kcpaul168 • 0
7
votes
2
replies
3.1k
views
False discovery rates in DEP
p-value FDR DEP
updated 4.6 years ago by ▴ 510 • written 5.1 years ago by ▴ 60
0
votes
2
replies
2.1k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 14 months ago by • 0 • written 4.8 years ago by ▴ 20
3
votes
2
replies
2.4k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
8.1 years ago • updated 7.9 years ago alex.gos90 ▴ 10
1
vote
2
replies
1.4k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.5 years ago by ▴ 220 • written 2.6 years ago by ▴ 10
1
vote
2
replies
2.6k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
6.0 years ago Rob • 0
0
votes
1
reply
1.9k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
Error in generating heatmap
dep
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
vote
1
reply
1.4k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 5.3 years ago by ▴ 510 • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.3k
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 5.2 years ago by 4.3k • written 5.2 years ago by • 0
0
votes
1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.4 years ago by 4.3k • written 3.4 years ago by • 0
0
votes
1
reply
1.0k
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
vote
1
reply
1.3k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
votes
0
replies
1.7k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
4.4 years ago barrypraveen • 0
0
votes
0
replies
1.5k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.3 years ago dparrine • 0
0
votes
0
replies
1.3k
views
DEP package - Understanding the results table
dep proteomics logFC
6.3 years ago rina ▴ 30
0
votes
0
replies
1.5k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.4 years ago tatabox • 0
0
votes
0
replies
1.4k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.6 years ago hele7 ▴ 20
0
votes
0
replies
481
views
Warning while loading DEP package
DEP
updated 21 months ago by 4.3k • written 21 months ago by • 0
0
votes
0
replies
1.4k
views
Introduction to DEP - data imputation
DEP impute
4.4 years ago catherine.li • 0
0
votes
0
replies
2.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.5 years ago by • 0
0
votes
0
replies
1.0k
views
Which package I can use?
MSnbase DAPAR DEP
5.2 years ago yueli7 ▴ 20
0
votes
0
replies
963
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.8 years ago aymanreffai • 0
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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