Showing : DEP • reset
2
votes
8
replies
2.4k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.4 years ago Wuschel ▴ 10
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
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
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
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
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
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
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
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
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
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
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
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
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
0
votes
2
replies
750
views
Error message trying to open downloaded package
error DEP
22 months ago kcpaul168 • 0
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
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
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
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
1
reply
763
views
Issue installing DEP package
DEP
updated 2.3 years ago by 4.1k • written 2.3 years ago by • 0
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
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
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
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
0
votes
0
replies
992
views
Introduction to DEP - data imputation
DEP impute
3.3 years ago catherine.li • 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
803
views
Which package I can use?
MSnbase DAPAR DEP
4.1 years ago yueli7 ▴ 20
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
0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.2 years ago dparrine • 0
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
0
replies
971
views
DEP package - Understanding the results table
dep proteomics logFC
5.2 years ago rina ▴ 30
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
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.3 years ago tatabox • 0
38 results • Page 1 of 1
Recent ...
Replies
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.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Hi Gordon, Thank you so much for this response. I went back and checked, and you are absolutely correct that it was shown in the settings b…
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
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