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dep
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0
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49
views
Warning while loading DEP package
DEP
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
0
votes
3
replies
265
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Laura
• 0
1
vote
2
replies
639
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 9 months ago by
Ram
▴ 190 • written 10 months ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
1.7k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 2.8 years ago by
barrypraveen
• 0
0
votes
0
replies
471
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
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 3.0 years ago by
hele7
▴ 20
0
votes
1
reply
419
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 13 months ago by
Basti
▴ 770 • written 13 months ago by
fuqichen1
• 0
0
votes
2
replies
532
views
Error message trying to open downloaded package
error
DEP
14 months ago
kcpaul168
• 0
0
votes
7
replies
3.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 20 months ago by
Malcolm Cook
★ 1.6k • written 2.1 years ago by
Tobias
▴ 40
0
votes
1
reply
573
views
Issue installing DEP package
DEP
updated 20 months ago by
shepherl
3.8k • written 20 months ago by
dheeraj.raya
• 0
0
votes
0
replies
775
views
Introduction to DEP - data imputation
DEP
impute
2.6 years ago
catherine.li
• 0
0
votes
0
replies
888
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
2.7 years ago
barrypraveen
• 0
0
votes
1
reply
832
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
pedarf
• 0
0
votes
1
reply
1.1k
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
7
votes
2
replies
1.9k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.8 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.4 years ago by
Alexei Leliavski
▴ 60
0
votes
0
replies
778
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago
hele7
▴ 20
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by
Basti
▴ 770 • written 3.0 years ago by
julie.hibbert
• 0
0
votes
3
replies
4.1k
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
7
replies
3.1k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
3.1 years ago
tpm
• 0
1
vote
4
replies
1.5k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
3.1 years ago
tpm
• 0
0
votes
4
replies
1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
3.1 years ago
rina
▴ 30
3
votes
7
replies
3.5k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by
Desiree.
▴ 10 • written 3.6 years ago by
hele7
▴ 20
0
votes
1
reply
778
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 3.4 years ago by
shepherl
3.8k • written 3.4 years ago by
tpm
• 0
3
votes
3
replies
955
views
se does not inherit from class SummarizedExperiment
DEP
3.4 years ago
yueli7
▴ 20
0
votes
0
replies
640
views
Which package I can use?
MSnbase
DAPAR
DEP
3.4 years ago
yueli7
▴ 20
1
vote
1
reply
842
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.5 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.5 years ago by
justindean9208
▴ 10
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 3.7 years ago by
Laurent Gatto
1.6k • written 3.7 years ago by
jp
• 0
0
votes
1
reply
719
views
Error in generating heatmap
dep
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
nkvnambiar
• 0
1
vote
2
replies
1.7k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
4.3 years ago
Rob
• 0
0
votes
0
replies
792
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.5 years ago
rina
▴ 30
0
votes
0
replies
929
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
4.6 years ago
dparrine
• 0
0
votes
0
replies
984
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.7 years ago
tatabox
• 0
2
votes
3
replies
1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.7 years ago by
arne.smits
▴ 70 • written 4.7 years ago by
Rob
• 0
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP
proteomics
updated 4.7 years ago by
arne.smits
▴ 70 • written 4.8 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
4.7 years ago
Wuschel
▴ 10
1
vote
1
reply
783
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
826599
▴ 10
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
6.4 years ago • updated 6.2 years ago
alex.gos90
▴ 10
2
votes
3
replies
2.1k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 6.4 years ago by
Laurent Gatto
1.6k • written 6.4 years ago by
serpalma.v
▴ 60
38 results • Page
1 of 1
Recent ...
Replies
Answer: Why p value inconsistent when using different number of pathway score?
by
ATpoint
★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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