Showing : dep • reset
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336
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Warning while loading DEP package
DEP
updated 13 months ago by 4.1k • written 13 months ago by • 0
0
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3
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1.0k
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 14 months ago by 52k • written 14 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 22 months ago by ▴ 220 • written 23 months ago by ▴ 10
0
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0
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782
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.1 years ago aymanreffai • 0
0
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1
reply
693
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
0
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2
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882
views
Error message trying to open downloaded package
error DEP
2.3 years ago kcpaul168 • 0
0
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1
reply
889
views
Issue installing DEP package
DEP
updated 2.8 years ago by 4.1k • written 2.8 years ago by • 0
0
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7
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5.0k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.8 years ago by ★ 1.6k • written 3.2 years ago by ▴ 40
0
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0
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1.1k
views
Introduction to DEP - data imputation
DEP impute
3.7 years ago catherine.li • 0
0
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0
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1.4k
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How to handle the imputation and normalisation?
Proteomics DEP limma
3.8 years ago barrypraveen • 0
0
votes
1
reply
1.2k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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1
reply
1.6k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
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0
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2.5k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.8 years ago by • 0
0
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0
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1.2k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.9 years ago hele7 ▴ 20
1
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3
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1.8k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.1 years ago by ▴ 780 • written 4.1 years ago by • 0
0
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2
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1.7k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 months ago by • 0 • written 4.1 years ago by ▴ 20
0
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3
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4.8k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.1 years ago by • 0 • written 4.3 years ago by • 0
1
vote
7
replies
3.9k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.2 years ago tpm • 0
1
vote
4
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2.1k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.2 years ago tpm • 0
0
votes
4
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1.5k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.2 years ago rina ▴ 30
3
votes
7
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4.2k
views
Error when loading DEP in RStudio
dep
updated 4.3 years ago by ▴ 10 • written 4.7 years ago by ▴ 20
7
votes
2
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2.7k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.9 years ago by ▴ 510 • written 4.5 years ago by ▴ 60
0
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1
reply
1.1k
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 4.5 years ago by 4.1k • written 4.5 years ago by • 0
3
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3
replies
1.4k
views
se does not inherit from class SummarizedExperiment
DEP
4.5 years ago yueli7 ▴ 20
0
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0
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885
views
Which package I can use?
MSnbase DAPAR DEP
4.5 years ago yueli7 ▴ 20
1
vote
1
reply
1.2k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.6 years ago by ▴ 510 • written 4.6 years ago by ▴ 10
1
vote
6
replies
3.9k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.8 years ago by 1.6k • written 4.8 years ago by • 0
0
votes
1
reply
1.0k
views
Error in generating heatmap
dep
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
1
vote
2
replies
2.2k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.3 years ago Rob • 0
0
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0
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1.1k
views
DEP package - Understanding the results table
dep proteomics logFC
5.6 years ago rina ▴ 30
0
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0
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1.3k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.7 years ago • updated 5.6 years ago dparrine • 0
0
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0
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1.3k
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.7 years ago tatabox • 0
2
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3
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1.7k
views
DEP package: error in plot_heatmap
DEP
updated 5.8 years ago by ▴ 70 • written 5.8 years ago by • 0
3
votes
3
replies
1.5k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.8 years ago by ▴ 70 • written 5.8 years ago by ▴ 510
2
votes
8
replies
2.7k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.8 years ago Wuschel ▴ 10
1
vote
1
reply
1.1k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
3
votes
2
replies
2.1k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.5 years ago • updated 7.3 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.7k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.5 years ago by 1.6k • written 7.5 years ago by ▴ 60
38 results • Page 1 of 1
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Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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