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MethylationArray
•
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0
votes
0
replies
133
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
6 weeks ago • updated 4 weeks ago
Giovanni Calice
▴ 160
0
votes
11
replies
674
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
mico
• 0
0
votes
1
reply
226
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 6 weeks ago by
belinda.phipson
▴ 40 • written 6 weeks ago by
s.malik
• 0
1
vote
6
replies
436
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
7 weeks ago
mico
• 0
1
vote
0
replies
144
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
7 weeks ago
BioinfoMug
• 0
1
vote
1
reply
255
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
david.cheishvili
• 0
0
votes
7
replies
409
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
sharangiiv
• 0
1
vote
2
replies
296
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
10 weeks ago
mico
• 0
1
vote
4
replies
419
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
10 weeks ago
mikat
• 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 6 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
0
votes
1
reply
700
views
EPIC v2 demo data from blood samples
MethylationArray
methylationArrayAnalysis
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
henry-keen
• 0
5
votes
5
replies
770
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
8 months ago
Jitendra
▴ 10
1
vote
1
reply
543
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
▴ 170 • written 12 months ago by
Grace
• 0
0
votes
1
reply
527
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
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 13 months ago by
Grace
• 0
0
votes
4
replies
988
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Grace
• 0
2
votes
1
reply
643
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
1.2k
views
Limma vs. lm for methylation data
limma
MethylationArrayData
MethylationArray
2.0 years ago
fluentin44
• 0
6
votes
6
replies
1.5k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray
limma
3.3 years ago • updated 3.2 years ago
MoltenLight
▴ 10
0
votes
0
replies
951
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.2 years ago
epibio
▴ 10
0
votes
0
replies
608
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
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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