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MethylationArray
•
reset
0
votes
0
replies
200
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
6 months ago
user_bioinfo
• 0
0
votes
0
replies
317
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
7 months ago
charlie.wright
• 0
0
votes
1
reply
330
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Anki
• 0
1
vote
2
replies
533
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
10 months ago • updated 9 months ago
Meghan
• 0
2
votes
1
reply
655
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
rae.alshammari
▴ 20
1
vote
2
replies
1.0k
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
12 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
650
views
Annotating DMRs
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
ramiro.barrantes
▴ 10
1
vote
1
reply
767
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Fateme
• 0
0
votes
3
replies
808
views
Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray
sesameData
sesame
updated 9 months ago by
alyssa-daniel
• 0 • written 13 months ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
1.7k
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
updated 3 months ago by
juansmurphy
• 0 • written 14 months ago by
hayleyw
• 0
0
votes
1
reply
869
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 9 months ago by
nereaherrera23
• 0 • written 14 months ago by
Mathu
• 0
0
votes
2
replies
2.0k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 16 months ago by
zhouwanding
▴ 20 • written 16 months ago by
Seungmin
• 0
3
votes
2
replies
1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Kim
• 0
1
vote
2
replies
2.3k
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
17 months ago • updated 16 months ago
Yveto
• 0
0
votes
0
replies
581
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
18 months ago
Giovanni Calice
▴ 160
1
vote
3
replies
2.1k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
18 months ago • updated 12 months ago
s.malik
• 0
0
votes
11
replies
1.7k
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 18 months ago by
Gordon Smyth
53k • written 19 months ago by
mico
• 0
1
vote
7
replies
1.6k
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
updated 11 months ago by
juansmurphy
• 0 • written 19 months ago by
mico
• 0
1
vote
1
reply
1.6k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
david.cheishvili
• 0
0
votes
7
replies
1.3k
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
sharangiiv
• 0
1
vote
2
replies
1.0k
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
19 months ago
mico
• 0
1
vote
4
replies
1.5k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
19 months ago
mikat
• 0
0
votes
1
reply
1.3k
views
EPIC v2 demo data from blood samples
MethylationArray
methylationArrayAnalysis
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
henry-keen
• 0
5
votes
5
replies
1.5k
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
2.1 years ago
Jitendra
▴ 10
1
vote
1
reply
1.0k
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 2.4 years ago by
belinda.phipson
▴ 40 • written 2.4 years ago by
Grace
• 0
2
votes
6
replies
1.9k
views
cpg.annotate() in DMRcate error
DNAMethylation
methylationArrayAnalysis
DMRcate
MethylationArrayData
MethylationArray
updated 2.4 years ago by
Tim Peters
▴ 230 • written 2.4 years ago by
Grace
• 0
0
votes
1
reply
1.0k
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Grace
• 0
0
votes
4
replies
1.9k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Grace
• 0
0
votes
5
replies
2.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 2.6 years ago by
Grace
• 0
2
votes
1
reply
1.0k
views
Limma model orientation
limma
methylation
MethylationArray
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
fluentin44
• 0
2
votes
2
replies
1.9k
views
Limma vs. lm for methylation data
limma
MethylationArrayData
MethylationArray
3.5 years ago • updated 3.4 years ago
fluentin44
• 0
0
votes
0
replies
1.4k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
4.7 years ago
epibio
▴ 10
6
votes
6
replies
2.3k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray
limma
4.7 years ago • updated 4.6 years ago
MoltenLight
▴ 10
2
votes
7
replies
3.7k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 23 months ago by
dorota.komar
• 0 • written 4.8 years ago by
Ankit
▴ 20
0
votes
0
replies
894
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
4.9 years ago
coobzie
• 0
35 results • Page
1 of 1
Recent ...
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Comment: EuroBioC2024 abstract submission is open!
by
leoblevins38
• 0
The difficulty of the game [Space Waves][1] gradually rises as it goes on. In order to help players become accustomed to the rhythm, early …
Answer: Sharing a collection of datasets in ExperimentHub
by
shepherl
4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure
by
Skyler
• 0
Am I using Bioc-devel?
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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