Showing : DEP • reset
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3
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508
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
11 weeks ago • updated 9 weeks ago Shajahan • 0
0
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0
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427
views
Warning while loading DEP package
DEP
updated 17 months ago by 4.2k • written 17 months ago by • 0
0
votes
3
replies
1.1k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 19 months ago by 53k • written 19 months ago by • 0
1
vote
2
replies
1.3k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.2 years ago by ▴ 220 • written 2.3 years ago by ▴ 10
0
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0
replies
873
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.5 years ago aymanreffai • 0
0
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1
reply
800
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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2
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1.0k
views
Error message trying to open downloaded package
error DEP
2.7 years ago kcpaul168 • 0
0
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1
reply
1.0k
views
Issue installing DEP package
DEP
updated 3.2 years ago by 4.2k • written 3.2 years ago by • 0
0
votes
7
replies
5.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.2 years ago by ★ 1.6k • written 3.6 years ago by ▴ 40
0
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0
replies
1.2k
views
Introduction to DEP - data imputation
DEP impute
4.1 years ago catherine.li • 0
0
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0
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1.5k
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How to handle the imputation and normalisation?
Proteomics DEP limma
4.2 years ago barrypraveen • 0
0
votes
1
reply
1.3k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
1
reply
1.8k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
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0
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2.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.2 years ago by • 0
0
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0
replies
1.3k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.3 years ago hele7 ▴ 20
1
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3
replies
1.9k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.5 years ago by ▴ 780 • written 4.5 years ago by • 0
0
votes
2
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1.9k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 11 months ago by • 0 • written 4.5 years ago by ▴ 20
0
votes
3
replies
5.0k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.5 years ago by • 0 • written 4.7 years ago by • 0
1
vote
7
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4.1k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.6 years ago tpm • 0
1
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4
replies
2.2k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.6 years ago tpm • 0
0
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4
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1.6k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.6 years ago rina ▴ 30
3
votes
7
replies
4.3k
views
Error when loading DEP in RStudio
dep
updated 4.7 years ago by ▴ 10 • written 5.1 years ago by ▴ 20
7
votes
2
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2.9k
views
False discovery rates in DEP
p-value FDR DEP
updated 4.3 years ago by ▴ 510 • written 4.9 years ago by ▴ 60
0
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1
reply
1.2k
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 4.9 years ago by 4.2k • written 4.9 years ago by • 0
3
votes
3
replies
1.5k
views
se does not inherit from class SummarizedExperiment
DEP
4.9 years ago yueli7 ▴ 20
0
votes
0
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968
views
Which package I can use?
MSnbase DAPAR DEP
4.9 years ago yueli7 ▴ 20
1
vote
1
reply
1.3k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 5.0 years ago by ▴ 510 • written 5.0 years ago by ▴ 10
1
vote
6
replies
4.1k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.2 years ago by 1.6k • written 5.2 years ago by • 0
0
votes
1
reply
1.1k
views
Error in generating heatmap
dep
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
1
vote
2
replies
2.5k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.7 years ago Rob • 0
0
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0
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1.2k
views
DEP package - Understanding the results table
dep proteomics logFC
6.0 years ago rina ▴ 30
0
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0
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1.4k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.1 years ago • updated 6.0 years ago dparrine • 0
0
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0
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1.4k
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.1 years ago tatabox • 0
2
votes
3
replies
1.8k
views
DEP package: error in plot_heatmap
DEP
updated 6.2 years ago by ▴ 70 • written 6.2 years ago by • 0
3
votes
3
replies
1.6k
views
Clarification of results tables in DEP
DEP proteomics
updated 6.2 years ago by ▴ 70 • written 6.2 years ago by ▴ 510
2
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8
replies
3.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.2 years ago Wuschel ▴ 10
1
vote
1
reply
1.2k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
3
votes
2
replies
2.2k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.9 years ago • updated 7.7 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.9k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.9 years ago by 1.6k • written 7.9 years ago by ▴ 60
39 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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