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
1
reply
573
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 5 days ago by
Simran
• 0 • written 23 months ago by
hele7
▴ 20
0
votes
1
reply
69
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 8 days ago by
Basti
▴ 700 • written 9 days ago by
fuqichen1
• 0
0
votes
2
replies
139
views
Error message trying to open downloaded package
error
DEP
7 weeks ago • updated 6 weeks ago
kcpaul168
• 0
0
votes
7
replies
1.9k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 7 months ago by
Malcolm Cook
★ 1.6k • written 12 months ago by
Tobias
▴ 40
0
votes
1
reply
220
views
Issue installing DEP package
DEP
updated 7 months ago by
shepherl
3.4k • written 7 months ago by
dheeraj.raya
• 0
0
votes
0
replies
403
views
Introduction to DEP - data imputation
DEP
impute
19 months ago
catherine.li
• 0
0
votes
0
replies
415
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
19 months ago
barrypraveen
• 0
0
votes
1
reply
415
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 20 months ago by
James W. MacDonald
62k • written 20 months ago by
pedarf
• 0
0
votes
1
reply
559
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 20 months ago by
bigomics.team
• 0 • written 20 months ago by
barrypraveen
• 0
0
votes
0
replies
884
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
20 months ago
barrypraveen
• 0
7
votes
2
replies
1.1k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 21 months ago by
António Miguel de Jesus Domingues
▴ 490 • written 2.3 years ago by
Alexei Leliavski
▴ 60
0
votes
0
replies
374
views
How to obtain log2 intensity per sample in DEP?
DEP
21 months ago
hele7
▴ 20
1
vote
3
replies
898
views
Error installing DEP in Rstudio on MacBook
DEP
updated 23 months ago by
Basti
▴ 700 • written 23 months ago by
julie.hibbert
• 0
0
votes
3
replies
2.9k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 2.0 years ago by
daniela.fuller
• 0 • written 2.2 years ago by
Tomaž
• 0
1
vote
7
replies
1.8k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
2.0 years ago
tpm
• 0
1
vote
4
replies
943
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
2.1 years ago
tpm
• 0
0
votes
4
replies
608
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
2.1 years ago
rina
▴ 20
3
votes
7
replies
2.8k
views
Error when loading DEP in RStudio
dep
updated 2.2 years ago by
Desiree.
▴ 10 • written 2.5 years ago by
hele7
▴ 20
0
votes
1
reply
500
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 2.4 years ago by
shepherl
3.4k • written 2.4 years ago by
tpm
• 0
3
votes
3
replies
575
views
se does not inherit from class SummarizedExperiment
DEP
2.4 years ago
yueli7
▴ 20
0
votes
0
replies
339
views
Which package I can use?
MSnbase
DAPAR
DEP
2.4 years ago
yueli7
▴ 20
1
vote
1
reply
545
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 2.5 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 2.5 years ago by
justindean9208
▴ 10
1
vote
6
replies
2.2k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 2.7 years ago by
Laurent Gatto
1.6k • written 2.7 years ago by
jp
• 0
0
votes
1
reply
423
views
Error in generating heatmap
dep
updated 2.9 years ago by
Kevin Blighe
3.8k • written 2.9 years ago by
nkvnambiar
• 0
1
vote
2
replies
1.2k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
3.2 years ago
Rob
• 0
0
votes
0
replies
472
views
DEP package - Understanding the results table
dep
proteomics
logFC
3.5 years ago
rina
▴ 20
0
votes
0
replies
607
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
3.5 years ago
dparrine
• 0
0
votes
0
replies
606
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
3.6 years ago
tatabox
• 0
2
votes
3
replies
850
views
DEP package: error in plot_heatmap
DEP
updated 3.6 years ago by
arne.smits
▴ 70 • written 3.6 years ago by
Rob
• 0
3
votes
3
replies
714
views
Clarification of results tables in DEP
DEP
proteomics
updated 3.7 years ago by
arne.smits
▴ 70 • written 3.7 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
8
replies
1.1k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
3.7 years ago
Wuschel
▴ 10
1
vote
1
reply
490
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 4.0 years ago by
James W. MacDonald
62k • written 4.0 years ago by
826599
▴ 10
3
votes
2
replies
1.0k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
5.3 years ago • updated 5.1 years ago
alex.gos90
▴ 10
2
votes
3
replies
1.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 5.3 years ago by
Laurent Gatto
1.6k • written 5.3 years ago by
serpalma.v
▴ 60
34 results • Page
1 of 1
Recent ...
Replies
Comment: how can I do gene differential analysis on data after vst
by
linouhao
▴ 20
Thanks a lot. so do you know when professor Gordon Smyth says 'Differential expression analysis of vst values can be performed by limma-t…
Comment: Help with Error in DiffBind
by
Rory Stark
★ 4.7k
Apologies. The first line should be result <- dba(sampleSheet=samples) I've gone back and edited previous replies to reflect this.
Answer: *** caught segfault *** , cause 'memory not mapped'
by
James W. MacDonald
62k
You are unfortunately running out of RAM. As you note, you could possibly use `frma`, after generating frozen vectors using the `frmaTools`…
Comment: Help with Error in DiffBind
by
Chris
• 0
Thanks Rory! result <- dba(samples) Error in if ((length(callers) == 1) & (callers[1] == "counts")) { : argument is of len…
Answer: Help with Error in DiffBind
by
Rory Stark
★ 4.7k
In your case, with only two replicates in each sample group, you can not perform a default analysis using only `dba.analyze()`. I suggest t…
Votes
Analyzing RNA-seq data by WGCNA
A: Analyzing RNA-seq data by WGCNA
Comment: Help with Error in DiffBind
WGCNA: Module preservation vs consensus analysis
WGCNA: Module preservation vs consensus analysis
Awards
• All
Supporter
to
linouhao
▴ 20
Popular Question
to
Seymoo
• 0
Popular Question
to
Wolfgang Huber
13k
Popular Question
to
shepherl
3.4k
Popular Question
to
dr
▴ 10
Locations
• All
France,
1 minute ago
United States,
2 minutes ago
United States,
4 minutes ago
WEHI, Melbourne, Australia,
13 minutes ago
Melbourne, Australia,
29 minutes ago
Traffic: 265 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