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DEP
•
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0
votes
0
replies
114
views
Warning while loading DEP package
DEP
updated 14 days ago by
shepherl
3.9k • written 14 days ago by
Namrata
• 0
0
votes
3
replies
281
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Laura
• 0
1
vote
2
replies
662
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 9 months ago by
Ram
▴ 200 • written 10 months ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
483
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
433
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 13 months ago by
Basti
▴ 780 • written 13 months ago by
fuqichen1
• 0
0
votes
2
replies
549
views
Error message trying to open downloaded package
error
DEP
14 months ago
kcpaul168
• 0
0
votes
1
reply
591
views
Issue installing DEP package
DEP
updated 21 months ago by
shepherl
3.9k • written 21 months ago by
dheeraj.raya
• 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
0
votes
0
replies
798
views
Introduction to DEP - data imputation
DEP
impute
2.7 years ago
catherine.li
• 0
0
votes
0
replies
904
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
2.7 years ago
barrypraveen
• 0
0
votes
1
reply
848
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
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
799
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
▴ 780 • written 3.0 years ago by
julie.hibbert
• 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 3.1 years ago by
hele7
▴ 20
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
3.2 years ago
rina
▴ 30
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.3 years ago by
Desiree.
▴ 10 • written 3.6 years ago by
hele7
▴ 20
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 3.4 years ago by
Alexei Leliavski
▴ 60
0
votes
1
reply
793
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
3
votes
3
replies
973
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago
yueli7
▴ 20
0
votes
0
replies
650
views
Which package I can use?
MSnbase
DAPAR
DEP
3.5 years ago
yueli7
▴ 20
1
vote
1
reply
855
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
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
1
reply
728
views
Error in generating heatmap
dep
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
nkvnambiar
• 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
0
votes
0
replies
800
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.6 years ago
rina
▴ 30
0
votes
0
replies
941
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
4.6 years ago
dparrine
• 0
0
votes
0
replies
999
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 4.8 years ago by
arne.smits
▴ 70 • written 4.8 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
4.8 years ago
Wuschel
▴ 10
1
vote
1
reply
795
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
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
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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