Showing : DEP • reset
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Warning while loading DEP package
DEP
updated 12 months ago by 4.1k • written 12 months ago by • 0
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3
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975
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 13 months ago by 52k • written 14 months ago by • 0
1
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2
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1.1k
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Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 21 months ago by ▴ 220 • written 22 months ago by ▴ 10
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767
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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
680
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
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2
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861
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Error message trying to open downloaded package
error DEP
2.2 years ago kcpaul168 • 0
0
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1
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877
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
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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 3.1 years ago by ▴ 40
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0
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1.1k
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Introduction to DEP - data imputation
DEP impute
3.6 years ago catherine.li • 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
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1.2k
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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
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1.6k
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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
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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
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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
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Error installing DEP in Rstudio on MacBook
DEP
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
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2
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1.7k
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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
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3
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4.8k
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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
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7
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3.9k
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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
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4
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2.1k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.1 years ago tpm • 0
0
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4
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1.5k
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.1 years ago rina ▴ 30
3
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7
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4.1k
views
Error when loading DEP in RStudio
dep
updated 4.2 years ago by ▴ 10 • written 4.6 years ago by ▴ 20
7
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2
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2.6k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.8 years ago by ▴ 510 • written 4.4 years ago by ▴ 60
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1
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1.0k
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I am using the DEP package example dataset, and I am getting this error on: plot_frequency(data_se)
DEP R Bioconductor Plot
updated 4.4 years ago by 4.1k • written 4.4 years ago by • 0
3
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3
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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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870
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Which package I can use?
MSnbase DAPAR DEP
4.5 years ago yueli7 ▴ 20
1
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1
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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
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6
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3.8k
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
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1
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1.0k
views
Error in generating heatmap
dep
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
1
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2
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2.2k
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Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.3 years ago Rob • 0
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0
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1.1k
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DEP package - Understanding the results table
dep proteomics logFC
5.5 years ago rina ▴ 30
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0
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1.3k
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DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.6 years ago dparrine • 0
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0
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1.3k
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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
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3
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1.5k
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Clarification of results tables in DEP
DEP proteomics
updated 5.7 years ago by ▴ 70 • written 5.8 years ago by ▴ 510
2
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8
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2.7k
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Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.7 years ago Wuschel ▴ 10
1
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1
reply
1.1k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
3
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2
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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
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3
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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: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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