Showing : DEP • reset
0
votes
0
replies
236
views
Warning while loading DEP package
DEP
updated 6 months ago by 4.1k • written 6 months ago by • 0
0
votes
3
replies
634
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 months ago by 51k • written 8 months ago by • 0
1
vote
2
replies
905
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 15 months ago by ▴ 210 • written 16 months ago by ▴ 10
0
votes
0
replies
654
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
18 months ago aymanreffai • 0
0
votes
1
reply
589
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 19 months ago by ▴ 780 • written 19 months ago by • 0
0
votes
2
replies
722
views
Error message trying to open downloaded package
error DEP
20 months ago kcpaul168 • 0
0
votes
1
reply
735
views
Issue installing DEP package
DEP
updated 2.2 years ago by 4.1k • written 2.2 years ago by • 0
0
votes
7
replies
4.2k
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 2.7 years ago by ▴ 40
0
votes
0
replies
957
views
Introduction to DEP - data imputation
DEP impute
3.2 years ago catherine.li • 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
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
0
votes
1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.3 years ago by • 0 • written 3.3 years ago by • 0
0
votes
0
replies
2.2k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.3 years ago by • 0
0
votes
0
replies
1.0k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.4 years ago hele7 ▴ 20
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
0
votes
2
replies
1.4k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 5 days ago by • 0 • written 3.5 years ago by ▴ 20
0
votes
3
replies
4.5k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.6 years ago by • 0 • written 3.8 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
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
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
7
replies
3.8k
views
Error when loading DEP in RStudio
dep
updated 3.8 years ago by ▴ 10 • written 4.1 years ago by ▴ 20
7
votes
2
replies
2.3k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.4 years ago by ▴ 510 • written 3.9 years ago by ▴ 60
0
votes
1
reply
931
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 4.0 years ago by 4.1k • written 4.0 years ago by • 0
3
votes
3
replies
1.2k
views
se does not inherit from class SummarizedExperiment
DEP
4.0 years ago yueli7 ▴ 20
0
votes
0
replies
781
views
Which package I can use?
MSnbase DAPAR DEP
4.0 years ago yueli7 ▴ 20
1
vote
1
reply
1.0k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.1 years ago by ▴ 510 • written 4.1 years ago by ▴ 10
1
vote
6
replies
3.5k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.3 years ago by 1.6k • written 4.3 years ago by • 0
0
votes
1
reply
887
views
Error in generating heatmap
dep
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.8 years ago Rob • 0
0
votes
0
replies
941
views
DEP package - Understanding the results table
dep proteomics logFC
5.1 years ago rina ▴ 30
0
votes
0
replies
1.1k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.1 years ago dparrine • 0
0
votes
0
replies
1.1k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.2 years ago tatabox • 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
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by ▴ 510
2
votes
8
replies
2.3k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.3 years ago Wuschel ▴ 10
1
vote
1
reply
955
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 10
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
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
38 results • Page 1 of 1
Recent ...
Replies
Comment: limma technical repeat correction by john • 0
@gordonsmyth Thank you for getting back to me and apologies for the confusion - `replicates_1` column indicates for a patient (cell line)…
Comment: Question about using LRT test for time course experiments with DESeq2 by Michael Love 42k
I understood your question above (at least I think so) and my response above remains relevant. > How can I get a coefficient/genes for th…
Answer: probe ID search for SNP (plink) by James W. MacDonald 67k
This site is meant to help people with questions about Bioconductor packages. Plink is not a Bioconductor package, or even an R package. Yo…
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore by Benjamin • 0
Thanks Mike, I will post here again when this issue gets resolved.
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore by Mike Smith ★ 6.5k
You are not the only biomaRt user to encounter this, and I contacted the Ensembl helpdesk. I got the reply below, which hopefully means it…
Votes
Answer: biomaRt rnorvegicus_gene_ensembl not available anymore
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Answer: Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichP
Comment: Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichP
Answer: Analysis of 2*4 factorial design
Awards • All
Popular Question to info ▴ 10
Scholar to James W. MacDonald 67k
Scholar to Gordon Smyth 51k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to FedeXandeR • 0
Locations • All
United States, 7 minutes ago
France, 7 minutes ago
Germany, 18 minutes ago
Germany, 19 minutes ago
Canada, 20 minutes ago
Traffic: 1148 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6