Showing : DEP • reset
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3
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525
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
3 months ago • updated 12 weeks ago Shajahan • 0
0
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0
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433
views
Warning while loading DEP package
DEP
updated 18 months ago by 4.2k • written 18 months ago by • 0
0
votes
3
replies
1.2k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 20 months ago by 53k • written 20 months ago by • 0
1
vote
2
replies
1.3k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.3 years ago by ▴ 220 • written 2.4 years ago by ▴ 10
0
votes
0
replies
896
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.6 years ago aymanreffai • 0
0
votes
1
reply
842
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 3.7 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Introduction to DEP - data imputation
DEP impute
4.2 years ago catherine.li • 0
0
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0
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1.6k
views
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 4.3 years ago by • 0 • written 4.3 years ago by • 0
0
votes
0
replies
2.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.3 years ago by • 0
0
votes
0
replies
1.3k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.4 years ago hele7 ▴ 20
1
vote
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
replies
1.9k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 12 months ago by • 0 • written 4.6 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 4.6 years ago by • 0 • written 4.8 years ago by • 0
1
vote
7
replies
4.2k
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
vote
4
replies
2.2k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.6 years ago tpm • 0
0
votes
4
replies
1.7k
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
4.4k
views
Error when loading DEP in RStudio
dep
updated 4.8 years ago by ▴ 10 • written 5.1 years ago by ▴ 20
7
votes
2
replies
2.9k
views
False discovery rates in DEP
p-value FDR DEP
updated 4.4 years ago by ▴ 510 • written 4.9 years ago by ▴ 60
0
votes
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 5.0 years ago by 4.2k • written 5.0 years ago by • 0
3
votes
3
replies
1.6k
views
se does not inherit from class SummarizedExperiment
DEP
5.0 years ago yueli7 ▴ 20
0
votes
0
replies
983
views
Which package I can use?
MSnbase DAPAR DEP
5.0 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 5.1 years ago by ▴ 510 • written 5.1 years ago by ▴ 10
1
vote
6
replies
4.1k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.3 years ago by 1.6k • written 5.3 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
5.8 years ago Rob • 0
0
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0
replies
1.2k
views
DEP package - Understanding the results table
dep proteomics logFC
6.1 years ago rina ▴ 30
0
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0
replies
1.4k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.1 years ago dparrine • 0
0
votes
0
replies
1.4k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.2 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 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 510
2
votes
8
replies
3.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.3 years ago Wuschel ▴ 10
1
vote
1
reply
1.2k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
3
votes
2
replies
2.3k
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
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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