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Showing :
DEP
•
reset
2
votes
8
replies
793
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
2.8 years ago
Wuschel
▴ 10
3
votes
7
replies
1.9k
views
Error when loading DEP in RStudio
dep
updated 16 months ago by
Desiree.
▴ 10 • written 20 months ago by
hele7
▴ 20
1
vote
7
replies
597
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
14 months ago
tpm
• 0
0
votes
6
replies
458
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 11 weeks ago by
Laurent Gatto
1.5k • written 11 weeks ago by
Tobias
▴ 30
1
vote
6
replies
1.3k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 22 months ago by
Laurent Gatto
1.5k • written 22 months ago by
jp
• 0
1
vote
4
replies
518
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
14 months ago
tpm
• 0
0
votes
4
replies
379
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
14 months ago
rina
▴ 20
1
vote
3
replies
619
views
Error installing DEP in Rstudio on MacBook
DEP
updated 13 months ago by
Basti
▴ 300 • written 13 months ago by
julie.hibbert
• 0
2
votes
3
replies
1.0k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 4.5 years ago by
Laurent Gatto
1.5k • written 4.5 years ago by
serpalma.v
▴ 60
3
votes
3
replies
559
views
Clarification of results tables in DEP
DEP
proteomics
updated 2.8 years ago by
arne.smits
▴ 70 • written 2.9 years ago by
António Miguel de Jesus Domingues
▴ 480
2
votes
3
replies
589
views
DEP package: error in plot_heatmap
DEP
updated 2.8 years ago by
arne.smits
▴ 70 • written 2.8 years ago by
Rob
• 0
3
votes
3
replies
398
views
se does not inherit from class SummarizedExperiment
DEP
18 months ago
yueli7
▴ 10
0
votes
3
replies
1.2k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 14 months ago by
daniela.fuller
• 0 • written 16 months ago by
Tomaž
• 0
1
vote
2
replies
950
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
2.4 years ago
Rob
• 0
7
votes
2
replies
683
views
False discovery rates in DEP
p-value
FDR
DEP
updated 11 months ago by
António Miguel de Jesus Domingues
▴ 480 • written 18 months ago by
Alexei Leliavski
▴ 60
3
votes
2
replies
858
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
4.5 years ago • updated 4.3 years ago
alex.gos90
▴ 10
1
vote
1
reply
349
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 19 months ago by
António Miguel de Jesus Domingues
▴ 480 • written 19 months ago by
justindean9208
▴ 10
0
votes
1
reply
270
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 10 months ago by
bigomics.team
• 0 • written 10 months ago by
barrypraveen
• 0
0
votes
1
reply
332
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 18 months ago by
shepherl
3.1k • written 18 months ago by
tpm
• 0
1
vote
1
reply
359
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 3.1 years ago by
James W. MacDonald
60k • written 3.1 years ago by
826599
▴ 10
0
votes
1
reply
222
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 9 months ago by
James W. MacDonald
60k • written 9 months ago by
pedarf
• 0
0
votes
1
reply
256
views
Error in generating heatmap
dep
updated 2.0 years ago by
Kevin Blighe
3.5k • written 2.0 years ago by
nkvnambiar
• 0
0
votes
0
replies
428
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
2.8 years ago
tatabox
• 0
0
votes
0
replies
190
views
How to obtain log2 intensity per sample in DEP?
DEP
11 months ago
hele7
▴ 20
0
votes
0
replies
212
views
Which package I can use?
MSnbase
DAPAR
DEP
18 months ago
yueli7
▴ 10
0
votes
0
replies
245
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
13 months ago
hele7
▴ 20
0
votes
0
replies
160
views
Introduction to DEP - data imputation
DEP
impute
8 months ago
catherine.li
• 0
0
votes
0
replies
449
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
10 months ago
barrypraveen
• 0
0
votes
0
replies
186
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
9 months ago
barrypraveen
• 0
0
votes
0
replies
301
views
DEP package - Understanding the results table
dep
proteomics
logFC
2.6 years ago
rina
▴ 20
0
votes
0
replies
424
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
2.7 years ago
dparrine
• 0
31 results • Page
1 of 1
Recent ...
Replies
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Comment: Rsamtools is not available for (for R version 4.0.2)
by
olinares-perdomo
• 0
I had the same problem (R 4.2.0) I used BiocManager::install("Rsamtools", force = TRUE) And it is working fine
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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