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MethylationArray
•
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0
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replies
111
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
24 days ago • updated 10 days ago
Giovanni Calice
▴ 160
0
votes
1
reply
179
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 24 days ago by
belinda.phipson
▴ 40 • written 25 days ago by
saad.malik
• 0
0
votes
11
replies
587
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 24 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
1
vote
0
replies
113
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
4 weeks ago
BioinfoMug
• 0
1
vote
6
replies
382
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
4 weeks ago
mico
• 0
1
vote
1
reply
212
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
david.cheishvili
• 0
0
votes
7
replies
352
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
sharangiiv
• 0
1
vote
2
replies
240
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
7 weeks ago
mico
• 0
1
vote
4
replies
365
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
7 weeks ago
mikat
• 0
0
votes
1
reply
642
views
EPIC v2 demo data from blood samples
MethylationArray
methylationArrayAnalysis
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
henry-keen
• 0
5
votes
5
replies
727
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
7 months ago
Jitendra
▴ 10
1
vote
1
reply
520
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 11 months ago by
belinda.phipson
▴ 40 • written 11 months ago by
Grace
• 0
2
votes
6
replies
1.0k
views
cpg.annotate() in DMRcate error
DNAMethylation
methylationArrayAnalysis
DMRcate
MethylationArrayData
MethylationArray
updated 11 months ago by
Tim Peters
▴ 160 • written 11 months ago by
Grace
• 0
0
votes
1
reply
493
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Grace
• 0
2
votes
7
replies
2.3k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 5 months ago by
dorota.komar
• 0 • written 3.3 years ago by
Ankit
▴ 20
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Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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