Showing : DEP • reset
0
votes
0
replies
110
views
Warning while loading DEP package
DEP
updated 13 days ago by 3.8k • written 13 days ago by • 0
0
votes
3
replies
278
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
1
vote
2
replies
662
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 9 months ago by ▴ 200 • written 10 months ago by ▴ 10
0
votes
0
replies
483
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
votes
1
reply
433
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
votes
2
replies
549
views
Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
0
votes
1
reply
591
views
Issue installing DEP package
DEP
updated 21 months ago by 3.8k • written 21 months ago by • 0
0
votes
7
replies
3.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 21 months ago by ★ 1.6k • written 2.2 years ago by ▴ 40
0
votes
0
replies
798
views
Introduction to DEP - data imputation
DEP impute
2.7 years ago catherine.li • 0
0
votes
0
replies
904
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
1
reply
848
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
0
votes
0
replies
1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
votes
0
replies
799
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
1
vote
3
replies
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
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
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
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
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
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.3 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.9 years ago by ▴ 510 • written 3.4 years ago by ▴ 60
0
votes
1
reply
793
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 3.5 years ago by 3.8k • written 3.5 years ago by • 0
3
votes
3
replies
972
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 20
0
votes
0
replies
650
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
1
vote
1
reply
855
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.6 years ago by ▴ 510 • 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
728
views
Error in generating heatmap
dep
updated 4.0 years ago by ★ 3.9k • written 4.0 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
votes
0
replies
800
views
DEP package - Understanding the results table
dep proteomics logFC
4.6 years ago rina ▴ 30
0
votes
0
replies
940
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago dparrine • 0
0
votes
0
replies
999
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
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
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by ▴ 510
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 years ago Wuschel ▴ 10
1
vote
1
reply
795
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.1 years ago by 65k • written 5.1 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
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards • All
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Locations • All
France, 5 minutes ago
United Kingdom, 7 minutes ago
United States, 12 minutes ago
Spain, 17 minutes ago
South Africa, 21 minutes ago
Traffic: 768 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6