Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DEP
•
reset
0
votes
3
replies
546
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
4 months ago • updated 3 months ago
Shajahan
• 0
0
votes
0
replies
448
views
Warning while loading DEP package
DEP
updated 19 months ago by
shepherl
4.2k • written 19 months ago by
Namrata
• 0
0
votes
3
replies
1.2k
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Laura
• 0
1
vote
2
replies
1.3k
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 2.4 years ago by
Ram
▴ 220 • written 2.4 years ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
928
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
2.6 years ago
aymanreffai
• 0
0
votes
1
reply
966
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
fuqichen1
• 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error
DEP
2.8 years ago
kcpaul168
• 0
0
votes
1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.3 years ago by
shepherl
4.2k • written 3.3 years ago by
dheeraj.raya
• 0
0
votes
7
replies
5.7k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 3.3 years ago by
Malcolm Cook
★ 1.6k • written 3.7 years ago by
Tobias
▴ 40
0
votes
0
replies
1.3k
views
Introduction to DEP - data imputation
DEP
impute
4.2 years ago
catherine.li
• 0
0
votes
0
replies
1.6k
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
4.3 years ago
barrypraveen
• 0
0
votes
1
reply
1.3k
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 4.3 years ago by
James W. MacDonald
68k • written 4.3 years ago by
pedarf
• 0
0
votes
1
reply
1.8k
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 4.4 years ago by
bigomics.team
• 0 • written 4.4 years ago by
barrypraveen
• 0
0
votes
0
replies
2.7k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 4.4 years ago by
barrypraveen
• 0
0
votes
0
replies
1.3k
views
How to obtain log2 intensity per sample in DEP?
DEP
4.5 years ago
hele7
▴ 20
1
vote
3
replies
1.9k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.6 years ago by
Basti
▴ 780 • written 4.6 years ago by
julie.hibbert
• 0
0
votes
2
replies
2.0k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by
Anni
• 0 • written 4.6 years ago by
hele7
▴ 20
0
votes
3
replies
5.1k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 4.7 years ago by
daniela.fuller
• 0 • written 4.9 years ago by
Tomaž
• 0
1
vote
7
replies
4.2k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
4.7 years ago
tpm
• 0
1
vote
4
replies
2.3k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
4.7 years ago
tpm
• 0
0
votes
4
replies
1.7k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
4.7 years ago
rina
▴ 30
3
votes
7
replies
4.4k
views
Error when loading DEP in RStudio
dep
updated 4.8 years ago by
Desiree.
▴ 10 • written 5.2 years ago by
hele7
▴ 20
7
votes
2
replies
3.0k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 4.4 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 5.0 years ago by
Alexei Leliavski
▴ 60
0
votes
1
reply
1.2k
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 5.0 years ago by
shepherl
4.2k • written 5.0 years ago by
tpm
• 0
3
votes
3
replies
1.6k
views
se does not inherit from class SummarizedExperiment
DEP
5.0 years ago
yueli7
▴ 20
0
votes
0
replies
1.0k
views
Which package I can use?
MSnbase
DAPAR
DEP
5.0 years ago
yueli7
▴ 20
1
vote
1
reply
1.3k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 5.1 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 5.1 years ago by
justindean9208
▴ 10
1
vote
6
replies
4.2k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 5.4 years ago by
Laurent Gatto
1.6k • written 5.4 years ago by
jp
• 0
0
votes
1
reply
1.2k
views
Error in generating heatmap
dep
updated 5.5 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
nkvnambiar
• 0
1
vote
2
replies
2.6k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
5.9 years ago
Rob
• 0
0
votes
0
replies
1.2k
views
DEP package - Understanding the results table
dep
proteomics
logFC
6.1 years ago
rina
▴ 30
0
votes
0
replies
1.4k
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
6.2 years ago
dparrine
• 0
0
votes
0
replies
1.4k
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
6.3 years ago
tatabox
• 0
2
votes
3
replies
1.8k
views
DEP package: error in plot_heatmap
DEP
updated 6.3 years ago by
arne.smits
▴ 70 • written 6.3 years ago by
Rob
• 0
3
votes
3
replies
1.7k
views
Clarification of results tables in DEP
DEP
proteomics
updated 6.3 years ago by
arne.smits
▴ 70 • written 6.4 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
8
replies
3.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
6.3 years ago
Wuschel
▴ 10
1
vote
1
reply
1.3k
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 6.6 years ago by
James W. MacDonald
68k • written 6.6 years ago by
826599
▴ 10
3
votes
2
replies
2.3k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
8.0 years ago • updated 7.8 years ago
alex.gos90
▴ 10
2
votes
3
replies
2.9k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 8.0 years ago by
Laurent Gatto
1.6k • written 8.0 years ago by
serpalma.v
▴ 60
39 results • Page
1 of 1
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
Gordon Smyth
53k
Popular Question
to
shepherl
4.2k
Popular Question
to
story.benjamin
▴ 20
Supporter
to
fabio.marroni
• 0
Popular Question
to
Guido Hooiveld
★ 4.1k
Locations
• All
WEHI, Melbourne, Australia,
14 minutes ago
Germany,
1 hour ago
Switzerland,
6 hours ago
Barcelona, Spain,
7 hours ago
The city by the bay,
8 hours ago
Traffic: 872 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