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MethylationArray
•
reset
0
votes
0
replies
86
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
13 days ago • updated 2 hours ago
Giovanni Calice
▴ 160
0
votes
1
reply
153
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 14 days ago by
belinda.phipson
▴ 40 • written 14 days ago by
saad.malik
• 0
0
votes
11
replies
547
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 14 days ago by
Gordon Smyth
50k • written 21 days ago by
mico
• 0
1
vote
0
replies
98
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
21 days ago
BioinfoMug
• 0
1
vote
6
replies
335
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
21 days ago
mico
• 0
1
vote
1
reply
181
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
david.cheishvili
• 0
0
votes
7
replies
337
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
sharangiiv
• 0
1
vote
2
replies
220
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
5 weeks ago
mico
• 0
1
vote
4
replies
342
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
6 weeks ago • updated 5 weeks ago
mikat
• 0
0
votes
1
reply
623
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
712
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
7 months ago
Jitendra
▴ 10
1
vote
1
reply
513
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 10 months ago by
belinda.phipson
▴ 40 • written 10 months ago by
Grace
• 0
2
votes
6
replies
988
views
cpg.annotate() in DMRcate error
DNAMethylation
methylationArrayAnalysis
DMRcate
MethylationArrayData
MethylationArray
updated 10 months ago by
Tim Peters
▴ 160 • written 10 months ago by
Grace
• 0
0
votes
1
reply
485
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
Grace
• 0
0
votes
4
replies
923
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
620
views
Limma model orientation
limma
methylation
MethylationArray
updated 22 months ago by
James W. MacDonald
65k • written 22 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
917
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
591
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
3.3 years ago
coobzie
• 0
22 results • Page
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
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