Showing : DEP • reset
7
votes
2
replies
1.5k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.3 years ago by ▴ 490 • written 2.8 years ago by ▴ 60
3
votes
3
replies
717
views
se does not inherit from class SummarizedExperiment
DEP
2.9 years ago yueli7 ▴ 20
3
votes
7
replies
3.1k
views
Error when loading DEP in RStudio
dep
updated 2.7 years ago by ▴ 10 • written 3.0 years ago by ▴ 20
3
votes
3
replies
892
views
Clarification of results tables in DEP
DEP proteomics
updated 4.2 years ago by ▴ 70 • written 4.2 years ago by ▴ 490
3
votes
2
replies
1.3k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
5.8 years ago • updated 5.6 years ago alex.gos90 ▴ 10
2
votes
3
replies
1.1k
views
DEP package: error in plot_heatmap
DEP
updated 4.1 years ago by ▴ 70 • written 4.2 years ago by • 0
2
votes
8
replies
1.5k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.2 years ago Wuschel ▴ 10
2
votes
3
replies
1.8k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 5.8 years ago by 1.6k • written 5.8 years ago by ▴ 60
1
vote
6
replies
2.8k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.2 years ago by 1.6k • written 3.2 years ago by • 0
1
vote
4
replies
1.2k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
2.6 years ago tpm • 0
1
vote
7
replies
2.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
2.6 years ago • updated 2.5 years ago tpm • 0
1
vote
2
replies
1.5k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
3.7 years ago Rob • 0
1
vote
1
reply
671
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.0 years ago by ▴ 490 • written 3.0 years ago by ▴ 10
1
vote
3
replies
1.1k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 2.4 years ago by ▴ 720 • written 2.4 years ago by • 0
1
vote
2
replies
276
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 10 weeks ago by ▴ 180 • written 3 months ago by ▴ 10
1
vote
1
reply
617
views
DEP p.val adjustment
DEP P.vals adjustment
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 10
0
votes
1
reply
621
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
votes
1
reply
822
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
225
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
5 months ago aymanreffai • 0
0
votes
2
replies
329
views
Error message trying to open downloaded package
error DEP
7 months ago kcpaul168 • 0
0
votes
1
reply
227
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 6 months ago by ▴ 720 • written 6 months ago by • 0
0
votes
0
replies
769
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.1 years ago tatabox • 0
0
votes
0
replies
758
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.0 years ago dparrine • 0
0
votes
0
replies
614
views
DEP package - Understanding the results table
dep proteomics logFC
4.0 years ago rina ▴ 20
0
votes
1
reply
554
views
Error in generating heatmap
dep
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
0
votes
0
replies
471
views
Which package I can use?
MSnbase DAPAR DEP
2.9 years ago yueli7 ▴ 20
0
votes
1
reply
610
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 2.9 years ago by 3.5k • written 2.9 years ago by • 0
0
votes
3
replies
3.7k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 2.5 years ago by • 0 • written 2.7 years ago by • 0
0
votes
0
replies
619
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.1 years ago barrypraveen • 0
0
votes
4
replies
847
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
2.6 years ago rina ▴ 20
0
votes
0
replies
581
views
How to obtain log2 intensity per sample in DEP?
DEP
2.3 years ago hele7 ▴ 20
0
votes
1
reply
376
views
Issue installing DEP package
DEP
updated 14 months ago by 3.5k • written 14 months ago by • 0
0
votes
7
replies
2.7k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 13 months ago by ★ 1.6k • written 19 months ago by ▴ 40
0
votes
1
reply
804
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 months ago by • 0 • written 2.5 years ago by ▴ 20
0
votes
0
replies
603
views
Introduction to DEP - data imputation
DEP impute
2.1 years ago catherine.li • 0
0
votes
0
replies
1.4k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.2 years ago by • 0
36 results • Page 1 of 1
Recent ...
Replies
Comment: Mixed up sample info with plotPCA by Michael Love 40k
Check colnames of count data. I think you are providing these in different order to DESeq2.
Comment: Mixed up sample info with plotPCA by sara.jacobson • 0
Ok, thank you. This is everything from my session: > library("ggplot2") > library("dplyr") Attaching package: 'dplyr' …
Answer: Gviz: UcscTrack and "GC Percent" information by Daniel E. Weeks ▴ 20
**Answer** In https://github.com/ivanek/Gviz/issues/71 an update that fixes this issue was documented - there it is stated that "…
Comment: Biostrings error at retrieving protein sequences by James W. MacDonald 63k
It depends on what kind of whitespace it is. If the whitespace is just a space, then it will work. But if it's a tab, it won't. ``` > gsub…
Comment: Biostrings error at retrieving protein sequences by nromerov • 0
If i write it like ```r gsub(" .*", "", names(protein_sequences)) ``` it will delet all the extra information if it is on the AAString…
Votes
Answer: Mouse to Human Genes using bioconductor
Mouse to Human Genes using bioconductor
Answer: Biostrings error at retrieving protein sequences
Answer: Biostrings error at retrieving protein sequences
Answer: How do I merge a list of GRanges?
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