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DEP
•
reset
2
votes
8
replies
2.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
4.8 years ago
Wuschel
▴ 10
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.3 years ago by
Desiree.
▴ 10 • written 3.7 years ago by
hele7
▴ 20
1
vote
7
replies
3.2k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
3.2 years ago
tpm
• 0
0
votes
7
replies
3.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 21 months ago by
Malcolm Cook
★ 1.6k • written 2.2 years ago by
Tobias
▴ 40
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 3.8 years ago by
Laurent Gatto
1.6k • written 3.8 years ago by
jp
• 0
0
votes
4
replies
1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
3.2 years ago
rina
▴ 30
1
vote
4
replies
1.6k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
3.2 years ago
tpm
• 0
0
votes
3
replies
317
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Laura
• 0
2
votes
3
replies
2.2k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 6.5 years ago by
Laurent Gatto
1.6k • written 6.5 years ago by
serpalma.v
▴ 60
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP
proteomics
updated 4.8 years ago by
arne.smits
▴ 70 • written 4.8 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
3
replies
1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.8 years ago by
arne.smits
▴ 70 • written 4.8 years ago by
Rob
• 0
3
votes
3
replies
986
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago
yueli7
▴ 20
0
votes
3
replies
4.2k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 3.1 years ago by
daniela.fuller
• 0 • written 3.3 years ago by
Tomaž
• 0
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.1 years ago by
Basti
▴ 780 • written 3.1 years ago by
julie.hibbert
• 0
1
vote
2
replies
1.8k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
4.3 years ago
Rob
• 0
1
vote
2
replies
686
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 10 months ago by
Ram
▴ 210 • written 11 months ago by
d.kozhevnikova
▴ 10
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
6.5 years ago • updated 6.3 years ago
alex.gos90
▴ 10
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.9 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.5 years ago by
Alexei Leliavski
▴ 60
0
votes
2
replies
564
views
Error message trying to open downloaded package
error
DEP
15 months ago
kcpaul168
• 0
1
vote
1
reply
862
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.6 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.6 years ago by
justindean9208
▴ 10
0
votes
1
reply
803
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 3.5 years ago by
shepherl
3.9k • written 3.5 years ago by
tpm
• 0
0
votes
1
reply
446
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
fuqichen1
• 0
0
votes
1
reply
596
views
Issue installing DEP package
DEP
updated 21 months ago by
shepherl
3.9k • written 21 months ago by
dheeraj.raya
• 0
1
vote
1
reply
802
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
826599
▴ 10
0
votes
1
reply
1.1k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by
Simran
• 0 • written 3.1 years ago by
hele7
▴ 20
0
votes
1
reply
857
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
pedarf
• 0
0
votes
1
reply
1.2k
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 2.8 years ago by
bigomics.team
• 0 • written 2.8 years ago by
barrypraveen
• 0
0
votes
1
reply
735
views
Error in generating heatmap
dep
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
nkvnambiar
• 0
0
votes
0
replies
811
views
Introduction to DEP - data imputation
DEP
impute
2.7 years ago
catherine.li
• 0
0
votes
0
replies
1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 2.8 years ago by
barrypraveen
• 0
0
votes
0
replies
662
views
Which package I can use?
MSnbase
DAPAR
DEP
3.5 years ago
yueli7
▴ 20
0
votes
0
replies
923
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
2.8 years ago
barrypraveen
• 0
0
votes
0
replies
1.0k
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.7 years ago
tatabox
• 0
0
votes
0
replies
824
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago
hele7
▴ 20
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
0
votes
0
replies
951
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
4.7 years ago • updated 4.6 years ago
dparrine
• 0
0
votes
0
replies
811
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.6 years ago
rina
▴ 30
0
votes
0
replies
497
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
13 months ago
aymanreffai
• 0
38 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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