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MethylationArray
•
reset
0
votes
0
replies
108
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
22 days ago • updated 8 days ago
Giovanni Calice
▴ 160
0
votes
1
reply
175
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 23 days ago by
belinda.phipson
▴ 40 • written 23 days ago by
saad.malik
• 0
0
votes
11
replies
578
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
1
vote
0
replies
111
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
374
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
4 weeks ago
mico
• 0
1
vote
1
reply
209
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
david.cheishvili
• 0
0
votes
7
replies
348
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
237
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
7 weeks ago
mico
• 0
1
vote
4
replies
363
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
640
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
725
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
7 months ago
Jitendra
▴ 10
1
vote
1
reply
517
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
490
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
0
votes
4
replies
937
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
Grace
• 0
0
votes
5
replies
1.1k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 12 months ago by
Grace
• 0
2
votes
1
reply
626
views
Limma model orientation
limma
methylation
MethylationArray
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
fluentin44
• 0
2
votes
2
replies
1.1k
views
Limma vs. lm for methylation data
limma
MethylationArrayData
MethylationArray
23 months ago
fluentin44
• 0
0
votes
0
replies
926
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.2 years ago
epibio
▴ 10
6
votes
6
replies
1.5k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray
limma
3.2 years ago • updated 3.1 years ago
MoltenLight
▴ 10
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
0
votes
0
replies
597
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
3.4 years ago
coobzie
• 0
22 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Answer: Merging featureCounts output for different species
by
Michael Love
41k
Bioconductor support site is for posting questions about software. Try biostars.
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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