Showing : DEP • reset
1
vote
6
replies
3.6k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.4 years ago by 1.6k • written 4.4 years ago by • 0
3
votes
2
replies
1.8k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.0 years ago • updated 6.8 years ago alex.gos90 ▴ 10
0
votes
1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
3
votes
7
replies
3.9k
views
Error when loading DEP in RStudio
dep
updated 3.9 years ago by ▴ 10 • written 4.2 years ago by ▴ 20
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.4 years ago by ▴ 70 • written 5.4 years ago by ▴ 510
0
votes
3
replies
719
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 9 months ago by 52k • written 9 months ago by • 0
2
votes
3
replies
2.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.0 years ago by 1.6k • written 7.0 years ago by ▴ 60
1
vote
1
reply
989
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
2
votes
3
replies
1.5k
views
DEP package: error in plot_heatmap
DEP
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by • 0
0
votes
1
reply
907
views
Error in generating heatmap
dep
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
1
vote
1
reply
1.1k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.2 years ago by ▴ 510 • written 4.2 years ago by ▴ 10
3
votes
3
replies
1.3k
views
se does not inherit from class SummarizedExperiment
DEP
4.1 years ago yueli7 ▴ 20
0
votes
3
replies
4.5k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.7 years ago by • 0 • written 3.9 years ago by • 0
1
vote
7
replies
3.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.7 years ago tpm • 0
0
votes
7
replies
4.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.3 years ago by ★ 1.6k • written 2.8 years ago by ▴ 40
0
votes
1
reply
1.0k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.4 years ago by 67k • written 3.4 years ago by • 0
1
vote
3
replies
1.6k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
0
votes
2
replies
750
views
Error message trying to open downloaded package
error DEP
22 months ago kcpaul168 • 0
0
votes
1
reply
610
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 20 months ago by ▴ 780 • written 20 months ago by • 0
0
votes
0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
3.3 years ago barrypraveen • 0
0
votes
4
replies
1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.8 years ago rina ▴ 30
1
vote
4
replies
1.9k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.8 years ago tpm • 0
1
vote
2
replies
952
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 17 months ago by ▴ 220 • written 17 months ago by ▴ 10
0
votes
0
replies
1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.5 years ago hele7 ▴ 20
0
votes
0
replies
259
views
Warning while loading DEP package
DEP
updated 7 months ago by 4.1k • written 7 months ago by • 0
0
votes
1
reply
763
views
Issue installing DEP package
DEP
updated 2.3 years ago by 4.1k • written 2.3 years ago by • 0
0
votes
0
replies
678
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
20 months ago aymanreffai • 0
0
votes
2
replies
1.5k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 weeks ago by • 0 • written 3.7 years ago by ▴ 20
0
votes
0
replies
992
views
Introduction to DEP - data imputation
DEP impute
3.3 years ago catherine.li • 0
0
votes
0
replies
971
views
DEP package - Understanding the results table
dep proteomics logFC
5.2 years ago rina ▴ 30
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.9 years ago Rob • 0
0
votes
0
replies
2.2k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.4 years ago by • 0
0
votes
0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.2 years ago dparrine • 0
2
votes
8
replies
2.4k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.4 years ago Wuschel ▴ 10
0
votes
0
replies
803
views
Which package I can use?
MSnbase DAPAR DEP
4.1 years ago yueli7 ▴ 20
0
votes
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.3 years ago tatabox • 0
0
votes
1
reply
959
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 4.1 years ago by 4.1k • written 4.1 years ago by • 0
7
votes
2
replies
2.4k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.5 years ago by ▴ 510 • written 4.0 years ago by ▴ 60
38 results • Page 1 of 1
Recent ...
Replies
Answer: Advice needed: Using limma for differential pathway analysis with continuous dis by Gordon Smyth 52k
limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts by Yang Liao ▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by ATpoint ★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by swbarnes2 ★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
Awards • All
Popular Question to Tadeoye ▴ 20
Teacher to Gordon Smyth 52k
Scholar to Aaron Lun ★ 28k
Teacher to Michael Love 43k
Popular Question to Dario Strbenac ★ 1.5k
Locations • All
WEHI, Melbourne, Australia, 6 minutes ago
United Kingdom, 14 minutes ago
India, 21 minutes ago
UPF, Barcelona, Spain, 31 minutes ago
Australia, 58 minutes ago
Traffic: 686 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