Showing : dep • reset
0
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3
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553
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
4 months ago Shajahan • 0
0
votes
0
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451
views
Warning while loading DEP package
DEP
updated 19 months ago by 4.2k • written 19 months ago by • 0
0
votes
3
replies
1.2k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
2
replies
1.3k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.4 years ago by ▴ 220 • written 2.5 years ago by ▴ 10
0
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0
replies
939
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.7 years ago aymanreffai • 0
0
votes
1
reply
972
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error DEP
2.8 years ago kcpaul168 • 0
0
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1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.3 years ago by 4.2k • written 3.3 years ago by • 0
0
votes
7
replies
5.8k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.3 years ago by ★ 1.6k • written 3.8 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Introduction to DEP - data imputation
DEP impute
4.3 years ago catherine.li • 0
0
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0
replies
1.6k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
4.3 years ago barrypraveen • 0
0
votes
1
reply
1.3k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
1
reply
1.8k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
0
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0
replies
2.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.4 years ago by • 0
0
votes
0
replies
1.3k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.5 years ago hele7 ▴ 20
1
vote
3
replies
1.9k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.6 years ago by ▴ 780 • written 4.6 years ago by • 0
0
votes
2
replies
2.0k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by • 0 • written 4.7 years ago by ▴ 20
0
votes
3
replies
5.1k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.7 years ago by • 0 • written 4.9 years ago by • 0
1
vote
7
replies
4.3k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.7 years ago tpm • 0
1
vote
4
replies
2.3k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.7 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
4.8 years ago rina ▴ 30
3
votes
7
replies
4.4k
views
Error when loading DEP in RStudio
dep
updated 4.9 years ago by ▴ 10 • written 5.2 years ago by ▴ 20
7
votes
2
replies
3.0k
views
False discovery rates in DEP
p-value FDR DEP
updated 4.5 years ago by ▴ 510 • written 5.0 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 5.1 years ago by 4.2k • written 5.1 years ago by • 0
3
votes
3
replies
1.6k
views
se does not inherit from class SummarizedExperiment
DEP
5.1 years ago yueli7 ▴ 20
0
votes
0
replies
1.0k
views
Which package I can use?
MSnbase DAPAR DEP
5.1 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 5.2 years ago by ▴ 510 • written 5.2 years ago by ▴ 10
1
vote
6
replies
4.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.4 years ago by 1.6k • written 5.4 years ago by • 0
0
votes
1
reply
1.2k
views
Error in generating heatmap
dep
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
1
vote
2
replies
2.6k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.9 years ago Rob • 0
0
votes
0
replies
1.2k
views
DEP package - Understanding the results table
dep proteomics logFC
6.2 years ago rina ▴ 30
0
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0
replies
1.4k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.2 years ago dparrine • 0
0
votes
0
replies
1.4k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.3 years ago tatabox • 0
2
votes
3
replies
1.9k
views
DEP package: error in plot_heatmap
DEP
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by • 0
3
votes
3
replies
1.7k
views
Clarification of results tables in DEP
DEP proteomics
updated 6.4 years ago by ▴ 70 • written 6.4 years ago by ▴ 510
2
votes
8
replies
3.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.4 years ago Wuschel ▴ 10
1
vote
1
reply
1.3k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 10
3
votes
2
replies
2.3k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
8.0 years ago • updated 7.8 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 8.0 years ago by 1.6k • written 8.0 years ago by ▴ 60
39 results • Page 1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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