Showing : DEP • reset
0
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82
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Warning while loading DEP package
DEP
updated 5 days ago by 3.8k • written 5 days ago by • 0
0
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3
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267
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
1
vote
2
replies
646
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 9 months ago by ▴ 190 • written 10 months ago by ▴ 10
0
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0
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1.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
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0
replies
474
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
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1
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1.1k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by • 0 • written 3.0 years ago by ▴ 20
0
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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 ▴ 780 • written 13 months ago by • 0
0
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2
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536
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Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
0
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7
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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 ★ 1.6k • written 2.1 years ago by ▴ 40
0
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1
reply
576
views
Issue installing DEP package
DEP
updated 20 months ago by 3.8k • written 20 months ago by • 0
0
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0
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785
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Introduction to DEP - data imputation
DEP impute
2.6 years ago catherine.li • 0
0
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0
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893
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How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
1
reply
835
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.7 years ago by 65k • written 2.7 years ago by • 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 • 0 • written 2.8 years ago by • 0
7
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2
replies
1.9k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.8 years ago by ▴ 490 • written 3.4 years ago by ▴ 60
0
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0
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781
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
1
vote
3
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1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
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 • 0 • written 3.3 years ago by • 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
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4
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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
3.1 years ago rina ▴ 30
3
votes
7
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3.6k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
0
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1
reply
782
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 3.8k • written 3.4 years ago by • 0
3
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3
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957
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 20
0
votes
0
replies
642
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
1
vote
1
reply
847
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.5 years ago by ▴ 490 • written 3.6 years ago by ▴ 10
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.8 years ago by 1.6k • written 3.8 years ago by • 0
0
votes
1
reply
722
views
Error in generating heatmap
dep
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 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
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0
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793
views
DEP package - Understanding the results table
dep proteomics logFC
4.5 years ago rina ▴ 30
0
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0
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932
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago dparrine • 0
0
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0
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989
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
2
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3
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1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.7 years ago by ▴ 70 • written 4.8 years ago by ▴ 490
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 10
1
vote
1
reply
784
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 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 1.6k • written 6.4 years ago by ▴ 60
38 results • Page 1 of 1
Recent ...
Replies
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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