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MethylationArray
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135
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
14 days ago
charlie.wright
• 0
0
votes
1
reply
152
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 29 days ago by
James W. MacDonald
68k • written 29 days ago by
Anki
• 0
1
vote
2
replies
354
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
12 weeks ago
Meghan
• 0
2
votes
1
reply
432
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
rae.alshammari
▴ 10
1
vote
2
replies
656
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
5 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
386
views
Annotating DMRs
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
ramiro.barrantes
▴ 10
1
vote
1
reply
489
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
Fateme
• 0
0
votes
3
replies
568
views
Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray
sesameData
sesame
updated 11 weeks ago by
alyssa-daniel
• 0 • written 5 months ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
675
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
written 7 months ago by
hayleyw
• 0
0
votes
1
reply
611
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 12 weeks ago by
nereaherrera23
• 0 • written 7 months ago by
Mathu
• 0
0
votes
2
replies
1.2k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 9 months ago by
zhouwanding
▴ 20 • written 9 months ago by
Seungmin
• 0
3
votes
2
replies
858
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 8 months ago by
Gordon Smyth
52k • written 9 months ago by
Kim
• 0
1
vote
2
replies
1.6k
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
9 months ago
Yveto
• 0
0
votes
0
replies
448
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
11 months ago
Giovanni Calice
▴ 160
1
vote
3
replies
1.7k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
11 months ago • updated 5 months ago
s.malik
• 0
0
votes
11
replies
1.4k
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 11 months ago by
Gordon Smyth
52k • written 12 months ago by
mico
• 0
1
vote
7
replies
1.3k
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
updated 4 months ago by
juansmurphy
• 0 • written 12 months ago by
mico
• 0
1
vote
1
reply
1.3k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
david.cheishvili
• 0
0
votes
7
replies
1.0k
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
sharangiiv
• 0
1
vote
2
replies
823
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
12 months ago
mico
• 0
1
vote
4
replies
1.2k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
12 months ago
mikat
• 0
0
votes
1
reply
1.2k
views
EPIC v2 demo data from blood samples
MethylationArray
methylationArrayAnalysis
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
henry-keen
• 0
5
votes
5
replies
1.2k
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
18 months ago
Jitendra
▴ 10
1
vote
1
reply
843
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 22 months ago by
belinda.phipson
▴ 40 • written 22 months ago by
Grace
• 0
2
votes
6
replies
1.6k
views
cpg.annotate() in DMRcate error
DNAMethylation
methylationArrayAnalysis
DMRcate
MethylationArrayData
MethylationArray
updated 22 months ago by
Tim Peters
▴ 230 • written 22 months ago by
Grace
• 0
0
votes
1
reply
815
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
Grace
• 0
0
votes
4
replies
1.6k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Grace
• 0
0
votes
5
replies
1.9k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 23 months ago by
Grace
• 0
2
votes
1
reply
897
views
Limma model orientation
limma
methylation
MethylationArray
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
fluentin44
• 0
2
votes
2
replies
1.7k
views
Limma vs. lm for methylation data
limma
MethylationArrayData
MethylationArray
2.9 years ago
fluentin44
• 0
0
votes
0
replies
1.2k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
4.1 years ago
epibio
▴ 10
6
votes
6
replies
2.0k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray
limma
4.1 years ago • updated 4.0 years ago
MoltenLight
▴ 10
2
votes
7
replies
3.2k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 16 months ago by
dorota.komar
• 0 • written 4.2 years ago by
Ankit
▴ 20
0
votes
0
replies
780
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
4.3 years ago
coobzie
• 0
34 results • Page
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Recent ...
Replies
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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