Showing : DEP • reset
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
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
3
votes
3
replies
957
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 20
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
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
1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.7 years ago by ▴ 70 • written 4.7 years 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
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 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
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
1
vote
1
reply
848
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.6 years ago by ▴ 490 • written 3.6 years ago by ▴ 10
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
1
vote
2
replies
648
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
1
vote
1
reply
787
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
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
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
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
1
reply
836
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
474
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
votes
2
replies
538
views
Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
0
votes
1
reply
421
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
3
replies
268
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
0
replies
989
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
0
votes
0
replies
933
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago dparrine • 0
0
votes
0
replies
795
views
DEP package - Understanding the results table
dep proteomics logFC
4.5 years ago rina ▴ 30
0
votes
1
reply
723
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
642
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
0
votes
1
reply
784
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
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
0
votes
0
replies
894
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 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
0
votes
0
replies
784
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 6 days ago by 3.8k • written 6 days ago by • 0
0
votes
1
reply
578
views
Issue installing DEP package
DEP
updated 20 months ago by 3.8k • written 20 months ago by • 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
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
0
replies
786
views
Introduction to DEP - data imputation
DEP impute
2.6 years ago catherine.li • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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