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dep
•
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2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
4.7 years ago
Wuschel
▴ 10
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by
Desiree.
▴ 10 • written 3.6 years ago by
hele7
▴ 20
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
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
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
3.1 years ago
rina
▴ 30
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
3
replies
268
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Laura
• 0
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
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
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
958
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago
yueli7
▴ 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
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
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
649
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
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
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
2
replies
538
views
Error message trying to open downloaded package
error
DEP
14 months ago
kcpaul168
• 0
1
vote
1
reply
849
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
▴ 490 • written 3.6 years ago by
justindean9208
▴ 10
0
votes
1
reply
785
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
0
votes
1
reply
421
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
1
reply
579
views
Issue installing DEP package
DEP
updated 20 months ago by
shepherl
3.8k • written 20 months ago by
dheeraj.raya
• 0
1
vote
1
reply
787
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
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
837
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
1
reply
723
views
Error in generating heatmap
dep
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
nkvnambiar
• 0
0
votes
0
replies
786
views
Introduction to DEP - data imputation
DEP
impute
2.6 years ago
catherine.li
• 0
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
642
views
Which package I can use?
MSnbase
DAPAR
DEP
3.5 years ago
yueli7
▴ 20
0
votes
0
replies
894
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
2.7 years ago
barrypraveen
• 0
0
votes
0
replies
989
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.7 years ago
tatabox
• 0
0
votes
0
replies
784
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago
hele7
▴ 20
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
0
votes
0
replies
933
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
4.6 years ago
dparrine
• 0
0
votes
0
replies
795
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.5 years ago
rina
▴ 30
0
votes
0
replies
474
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
38 results • Page
1 of 1
Recent ...
Replies
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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