Showing : DEP • reset
0
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3
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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
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
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
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
1
vote
7
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2.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
2.5 years ago tpm • 0
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
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
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
2
votes
8
replies
1.5k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.2 years ago Wuschel ▴ 10
0
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0
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1.3k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.2 years ago by • 0
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
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
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
2
votes
3
replies
1.0k
views
DEP package: error in plot_heatmap
DEP
updated 4.1 years ago by ▴ 70 • written 4.1 years ago by • 0
3
votes
3
replies
890
views
Clarification of results tables in DEP
DEP proteomics
updated 4.2 years ago by ▴ 70 • written 4.2 years ago by ▴ 490
0
votes
4
replies
844
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
2.6 years ago rina ▴ 20
0
votes
1
reply
816
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
1
reply
800
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
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0
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768
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.1 years ago tatabox • 0
0
votes
0
replies
755
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.0 years ago dparrine • 0
3
votes
3
replies
711
views
se does not inherit from class SummarizedExperiment
DEP
2.9 years ago yueli7 ▴ 20
1
vote
1
reply
668
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
0
votes
1
reply
619
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
1
vote
1
reply
615
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
0
replies
612
views
DEP package - Understanding the results table
dep proteomics logFC
4.0 years ago rina ▴ 20
0
votes
0
replies
611
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.1 years ago barrypraveen • 0
0
votes
1
reply
609
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
0
replies
600
views
Introduction to DEP - data imputation
DEP impute
2.1 years ago catherine.li • 0
0
votes
0
replies
578
views
How to obtain log2 intensity per sample in DEP?
DEP
2.3 years ago hele7 ▴ 20
0
votes
1
reply
551
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
469
views
Which package I can use?
MSnbase DAPAR DEP
2.9 years ago yueli7 ▴ 20
0
votes
1
reply
375
views
Issue installing DEP package
DEP
updated 13 months ago by 3.5k • written 13 months ago by • 0
0
votes
2
replies
326
views
Error message trying to open downloaded package
error DEP
7 months ago kcpaul168 • 0
1
vote
2
replies
269
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
0
votes
1
reply
221
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
221
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
5 months ago aymanreffai • 0
36 results • Page 1 of 1
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Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC by James W. MacDonald 63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Comment: shinyMethyl - saving the file by dorota.komar • 0
I tried printing the page as pdf, unfortunately I get the same problem. I guess for now, I will need to save the graphs separately :) Than…
Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by Mike Smith ★ 6.1k
I'll echo James' suggestion to use the GRCh37 mirror. Most mirrors only have a guaranteed lifetime of 5 years from Ensembl, although it se…
Votes
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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