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DNAMethylation
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3
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5
replies
2.1k
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Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
updated 5 weeks ago by
sup0903
• 0 • written 3.3 years ago by
Hongbii
• 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
176
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 24 days ago by
saad.malik
• 0
0
votes
4
replies
283
views
Seeking Strategies for Managing Duplicate CpG Entries in EPIC v2 Manifest
DNAMethylation
EPICv2
IlluminaHumanMethylationEPICmanifest
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
rae.alshammari
▴ 10
1
vote
4
replies
287
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
3
votes
8
replies
1.3k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
2.8 years ago
rtrivedi1
▴ 10
2
votes
6
replies
878
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 12 months ago by
belinda.phipson
▴ 40 • written 12 months ago by
Joana
• 0
0
votes
1
reply
125
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 11 days ago by
Simon Pearce
• 0 • written 7 weeks ago by
User3088
• 0
0
votes
1
reply
457
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
11 months ago
Grace
• 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
0
replies
497
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
19 months ago
calen.p.ryan
• 0
11 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
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
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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James W. MacDonald
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Pierre Lindenbaum
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Gordon Smyth
50k
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