Showing : DEP • reset
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
3.5k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by ▴ 10 • written 3.6 years ago by ▴ 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 ★ 1.6k • written 2.1 years ago by ▴ 40
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.7 years ago by 1.6k • written 3.7 years ago by • 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
261
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 weeks ago by 50k • written 7 weeks ago by • 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 1.6k • written 6.4 years ago by ▴ 60
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
3
replies
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
953
views
se does not inherit from class SummarizedExperiment
DEP
3.4 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 • 0 • written 3.3 years ago by • 0
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by ▴ 760 • written 3.0 years ago by • 0
1
vote
2
replies
1.7k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
1
vote
2
replies
636
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
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 ▴ 490 • written 3.4 years ago by ▴ 60
0
votes
2
replies
530
views
Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
1
vote
1
reply
841
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.5 years ago by ▴ 490 • written 3.5 years ago by ▴ 10
0
votes
1
reply
775
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
0
votes
1
reply
416
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
votes
1
reply
572
views
Issue installing DEP package
DEP
updated 20 months ago by 3.8k • written 20 months ago by • 0
1
vote
1
reply
781
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 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 • 0 • written 3.0 years ago by ▴ 20
0
votes
1
reply
829
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 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
1
reply
715
views
Error in generating heatmap
dep
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 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 • 0
0
votes
0
replies
636
views
Which package I can use?
MSnbase DAPAR DEP
3.4 years ago yueli7 ▴ 20
0
votes
0
replies
886
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
0
replies
982
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
0
votes
0
replies
776
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
0
votes
0
replies
927
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago • updated 4.5 years ago dparrine • 0
0
votes
0
replies
790
views
DEP package - Understanding the results table
dep proteomics logFC
4.5 years ago rina ▴ 30
0
votes
0
replies
466
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
votes
0
replies
771
views
Introduction to DEP - data imputation
DEP impute
2.6 years ago catherine.li • 0
37 results • Page 1 of 1
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Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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