Showing : dep • reset
0
votes
3
replies
580
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
5 months ago Shajahan • 0
0
votes
0
replies
470
views
Warning while loading DEP package
DEP
updated 21 months ago by 4.2k • written 21 months ago by • 0
0
votes
3
replies
1.3k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 22 months ago by 53k • written 22 months ago by • 0
1
vote
2
replies
1.4k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 2.5 years ago by ▴ 220 • written 2.6 years ago by ▴ 10
0
votes
0
replies
958
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
1.0k
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error DEP
2.9 years ago kcpaul168 • 0
0
votes
1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.4 years ago by 4.2k • written 3.4 years ago by • 0
0
votes
7
replies
6.0k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.4 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
4.4 years ago catherine.li • 0
0
votes
0
replies
1.7k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
4.4 years ago barrypraveen • 0
0
votes
1
reply
1.4k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
votes
1
reply
1.9k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
0
votes
0
replies
2.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 4.5 years ago by • 0
0
votes
0
replies
1.4k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.6 years ago hele7 ▴ 20
1
vote
3
replies
1.9k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.7 years ago by ▴ 780 • written 4.7 years ago by • 0
0
votes
2
replies
2.0k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 14 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 4.8 years ago by • 0 • written 5.0 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
4.8 years ago tpm • 0
1
vote
4
replies
2.3k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.8 years ago tpm • 0
0
votes
4
replies
1.8k
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 5.0 years ago by ▴ 10 • written 5.3 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 5.1 years ago by ▴ 60
0
votes
1
reply
1.3k
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
5.2 years ago yueli7 ▴ 20
0
votes
0
replies
1.0k
views
Which package I can use?
MSnbase DAPAR DEP
5.2 years ago yueli7 ▴ 20
1
vote
1
reply
1.4k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 5.3 years ago by ▴ 510 • written 5.3 years ago by ▴ 10
1
vote
6
replies
4.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 5.5 years ago by 1.6k • written 5.5 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
6.0 years ago Rob • 0
0
votes
0
replies
1.2k
views
DEP package - Understanding the results table
dep proteomics logFC
6.3 years ago rina ▴ 30
0
votes
0
replies
1.5k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
6.3 years ago dparrine • 0
0
votes
0
replies
1.5k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.4 years ago tatabox • 0
2
votes
3
replies
1.9k
views
DEP package: error in plot_heatmap
DEP
updated 6.4 years ago by ▴ 70 • written 6.4 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 6.5 years ago by ▴ 510
2
votes
8
replies
3.1k
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 6.8 years ago by 68k • written 6.8 years ago by ▴ 10
3
votes
2
replies
2.4k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
8.1 years ago • updated 7.9 years ago alex.gos90 ▴ 10
2
votes
3
replies
3.0k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 8.1 years ago by 1.6k • written 8.1 years ago by ▴ 60
39 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Teacher to Michael Love 43k
Popular Question to lianov • 0
Locations • All
WEHI, Melbourne, Australia, 3 hours ago
United States, 4 hours ago
United States, 5 hours ago
Barcelona, Spain, 5 hours ago
United States, 6 hours ago
Traffic: 1142 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