Showing : DEP • reset
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
0
votes
7
replies
4.1k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.2 years ago by ★ 1.6k • written 2.6 years ago by ▴ 40
3
votes
7
replies
3.8k
views
Error when loading DEP in RStudio
dep
updated 3.7 years ago by ▴ 10 • written 4.1 years ago by ▴ 20
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
1
vote
7
replies
3.5k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.6 years ago tpm • 0
2
votes
3
replies
2.4k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 6.9 years ago by 1.6k • written 6.9 years ago by ▴ 60
2
votes
8
replies
2.3k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.2 years ago Wuschel ▴ 10
7
votes
2
replies
2.3k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.3 years ago by ▴ 510 • written 3.9 years ago by ▴ 60
0
votes
0
replies
2.1k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.2 years ago by • 0
1
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2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.7 years ago Rob • 0
1
vote
4
replies
1.8k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.6 years ago tpm • 0
3
votes
2
replies
1.7k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.9 years ago • updated 6.7 years ago alex.gos90 ▴ 10
1
vote
3
replies
1.6k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
2
votes
3
replies
1.4k
views
DEP package: error in plot_heatmap
DEP
updated 5.2 years ago by ▴ 70 • written 5.2 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
0
votes
1
reply
1.3k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 18 months ago by • 0 • written 3.5 years ago by ▴ 20
0
votes
4
replies
1.3k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.6 years ago rina ▴ 30
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.2 years ago by ▴ 70 • written 5.2 years ago by ▴ 510
3
votes
3
replies
1.2k
views
se does not inherit from class SummarizedExperiment
DEP
3.9 years ago yueli7 ▴ 20
0
votes
0
replies
1.1k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.1 years ago tatabox • 0
0
votes
0
replies
1.1k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.1 years ago • updated 5.0 years ago dparrine • 0
0
votes
0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
3.2 years ago barrypraveen • 0
0
votes
0
replies
1.0k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.3 years ago hele7 ▴ 20
1
vote
1
reply
1.0k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.0 years ago by ▴ 510 • written 4.0 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.2 years ago by 67k • written 3.2 years ago by • 0
1
vote
1
reply
947
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.5 years ago by 67k • written 5.5 years ago by ▴ 10
0
votes
0
replies
937
views
Introduction to DEP - data imputation
DEP impute
3.1 years ago catherine.li • 0
0
votes
0
replies
927
views
DEP package - Understanding the results table
dep proteomics logFC
5.0 years ago rina ▴ 30
0
votes
1
reply
922
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 3.9 years ago by 4.0k • written 3.9 years ago by • 0
1
vote
2
replies
884
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 15 months ago by ▴ 210 • written 15 months ago by ▴ 10
0
votes
1
reply
875
views
Error in generating heatmap
dep
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
votes
0
replies
773
views
Which package I can use?
MSnbase DAPAR DEP
3.9 years ago yueli7 ▴ 20
0
votes
1
reply
725
views
Issue installing DEP package
DEP
updated 2.2 years ago by 4.0k • written 2.2 years ago by • 0
0
votes
2
replies
708
views
Error message trying to open downloaded package
error DEP
20 months ago kcpaul168 • 0
0
votes
0
replies
635
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
18 months ago aymanreffai • 0
0
votes
3
replies
595
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
1
reply
581
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
votes
0
replies
229
views
Warning while loading DEP package
DEP
updated 5 months ago by 4.0k • written 5 months ago by • 0
38 results • Page 1 of 1
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Comment: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable by gabry.scata ▴ 10
Hi James, and thank you so much for your quick reply! That's great to know that I have installed successfully the packages i wanted. What …
Comment: pathview error "negative length vectors are not allowed by Evan • 0
Same for N-glycan metabolism-- fails with `same.layer = TRUE` , smudges and comet-like shading with `same.layer = FALSE`, crowded web with …
Comment: How to conduct maSigPro analysis with only one condition? by James W. MacDonald 67k
Technically it's fitting an analysis of deviance (ANODEV) test, but the principle is the same - deviance, like the likelihood, measures goo…
Comment: How to conduct maSigPro analysis with only one condition? by James W. MacDonald 67k
Yeah, it's fine. What `maSigPro` does in this case is to reformulate the data. Your design has columns that are not useful, and `maSigPro` …
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable by James W. MacDonald 67k
You have installed the packages you wanted: ``` package BiocVersion successfully unpacked and MD5 sums checked package LEA success…
Votes
Comment: How to conduct maSigPro analysis with only one condition?
Comment: How to conduct maSigPro analysis with only one condition?
Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
Answer: How to conduct maSigPro analysis with only one condition?
Answer: How to conduct maSigPro analysis with only one condition?
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