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dna methylation
•
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0
votes
1
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1.2k
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.9 years ago
grayapply2009
• 0
1
vote
2
replies
2.5k
views
WGCNA on methylation data
normalization
DNA methylation
WGCNA
updated 5.7 years ago by
Peter Langfelder
★ 3.0k • written 5.7 years ago by
enora.fremy
• 0
1
vote
2
replies
1.2k
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 6.2 years ago by
Lukas Chavez
▴ 570 • written 6.2 years ago by
mtefit
• 0
7
votes
7
replies
1.9k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 6.3 years ago by
Sean Davis
21k • written 6.3 years ago by
RichardJActon
▴ 50
1
vote
2
replies
1.6k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
6.6 years ago
peter.fransquet
• 0
0
votes
0
replies
906
views
iEVORA wrapping up error
differential variability
dna methylation
iEVORA
DVP
6.8 years ago
poojitha.stemcell
▴ 10
0
votes
0
replies
1.2k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
7.0 years ago
gabrielrfries
• 0
0
votes
1
reply
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 7.2 years ago by
Gordon Smyth
52k • written 7.2 years ago by
ahmad.moousavi
• 0
2
votes
5
replies
2.2k
views
Error when prepare the TCGAdata
tcgabiolinks
dna methylation
updated 7.2 years ago by
Marcel Ramos
700 • written 7.2 years ago by
michaelwxf2012
• 0
1
vote
1
reply
2.1k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 7.4 years ago by
James W. MacDonald
68k • written 7.4 years ago by
skids121
• 0
0
votes
0
replies
1.4k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV
minfi
preprocessing
dna methylation
7.9 years ago
Thomas
• 0
1
vote
2
replies
1.2k
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray
HM450
dna methylation
cohcap
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.3k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
fleur_p90
• 0
13 results • Page
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Recent ...
Replies
Answer: WGCNA with paired samples
by
Ivo
• 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2
by
ATpoint
★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability?
by
Bradley
• 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
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…
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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