Showing : DEP • reset
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328
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Warning while loading DEP package
DEP
updated 12 months ago by 4.1k • written 12 months ago by • 0
0
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3
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980
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 14 months ago by 52k • written 14 months ago by • 0
1
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2
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1.1k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 21 months ago by ▴ 220 • written 22 months ago by ▴ 10
0
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0
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771
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.0 years ago aymanreffai • 0
0
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1
reply
685
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
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2
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869
views
Error message trying to open downloaded package
error DEP
2.2 years ago kcpaul168 • 0
0
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1
reply
883
views
Issue installing DEP package
DEP
updated 2.7 years ago by 4.1k • written 2.7 years ago by • 0
0
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7
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5.0k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.7 years ago by ★ 1.6k • written 3.2 years ago by ▴ 40
0
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0
replies
1.1k
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Introduction to DEP - data imputation
DEP impute
3.7 years ago catherine.li • 0
0
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0
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1.3k
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How to handle the imputation and normalisation?
Proteomics DEP limma
3.7 years ago barrypraveen • 0
0
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1
reply
1.2k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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1
reply
1.6k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
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0
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2.5k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.8 years ago by • 0
0
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0
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1.2k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.9 years ago hele7 ▴ 20
1
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3
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1.8k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
0
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2
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1.7k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 months ago by • 0 • written 4.0 years ago by ▴ 20
0
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3
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4.8k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.1 years ago by • 0 • written 4.3 years ago by • 0
1
vote
7
replies
3.9k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.1 years ago tpm • 0
1
vote
4
replies
2.1k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.1 years ago tpm • 0
0
votes
4
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1.5k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.1 years ago rina ▴ 30
3
votes
7
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4.1k
views
Error when loading DEP in RStudio
dep
updated 4.3 years ago by ▴ 10 • written 4.6 years ago by ▴ 20
7
votes
2
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2.7k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.8 years ago by ▴ 510 • written 4.4 years ago by ▴ 60
0
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1
reply
1.1k
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 4.5 years ago by 4.1k • written 4.5 years ago by • 0
3
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3
replies
1.4k
views
se does not inherit from class SummarizedExperiment
DEP
4.5 years ago yueli7 ▴ 20
0
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0
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872
views
Which package I can use?
MSnbase DAPAR DEP
4.5 years ago yueli7 ▴ 20
1
vote
1
reply
1.2k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.6 years ago by ▴ 510 • written 4.6 years ago by ▴ 10
1
vote
6
replies
3.9k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.8 years ago by 1.6k • written 4.8 years ago by • 0
0
votes
1
reply
1.0k
views
Error in generating heatmap
dep
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
1
vote
2
replies
2.2k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.3 years ago Rob • 0
0
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0
replies
1.1k
views
DEP package - Understanding the results table
dep proteomics logFC
5.6 years ago rina ▴ 30
0
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0
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1.3k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.6 years ago dparrine • 0
0
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0
replies
1.3k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.7 years ago tatabox • 0
2
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3
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1.7k
views
DEP package: error in plot_heatmap
DEP
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by • 0
3
votes
3
replies
1.5k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.8 years ago by ▴ 70 • written 5.8 years ago by ▴ 510
2
votes
8
replies
2.7k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.8 years ago Wuschel ▴ 10
1
vote
1
reply
1.1k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
3
votes
2
replies
2.0k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.4 years ago • updated 7.2 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.7k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.4 years ago by 1.6k • written 7.4 years ago by ▴ 60
38 results • Page 1 of 1
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Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
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