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EPIC
•
reset
0
votes
0
replies
747
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
2.2 years ago
Jitendra
▴ 10
0
votes
2
replies
1.4k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
5.1 years ago • updated 4.6 years ago
Nala
• 0
2
votes
1
reply
1.3k
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
5.1 years ago
Zach Roe
▴ 10
1
vote
1
reply
1.3k
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
whyw6948
• 0
1
vote
3
replies
1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.3 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
1.1k
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 5.3 years ago by
Yuan Tian
▴ 90 • written 5.3 years ago by
cherlyn.t
• 0
2
votes
16
replies
3.8k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 5.4 years ago by
Yuan Tian
▴ 290 • written 5.4 years ago by
Ankit
▴ 20
3
votes
5
replies
1.9k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
yoursbassanio
▴ 10
0
votes
4
replies
2.3k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 2.3 years ago by
shuo
• 0 • written 5.7 years ago by
enora.fremy
• 0
0
votes
1
reply
2.6k
views
How to analyse 450k and EPIC methylation data together?
minfi
450k
EPIC
analysis
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
maduran
• 0
0
votes
3
replies
1.5k
views
Limma for cell components effect on response
450k
EPIC
minfi
limma
cell components
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
antgomo
• 0
1
vote
3
replies
1.6k
views
Obtaining annotated results from rnbeads
rnbeads
EPIC
updated 5.9 years ago by
mscherer
▴ 50 • written 6.0 years ago by
Mark Dunning
★ 1.1k
0
votes
0
replies
1.5k
views
Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
6.2 years ago
firestar
▴ 20
0
votes
0
replies
1.0k
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
6.2 years ago
firestar
▴ 20
2
votes
1
reply
1.7k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 6.5 years ago by
Yuan Tian
▴ 290 • written 6.5 years ago by
D
▴ 10
0
votes
2
replies
2.7k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP
Normalization
FunctionalNormalization
methylation
EPIC
6.6 years ago
yuabrahamliu
• 0
5
votes
9
replies
2.2k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
c.bettencourt
• 0
0
votes
0
replies
1.2k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
6.7 years ago
peter.fransquet
• 0
0
votes
3
replies
1.9k
views
Minfi error when using force=TRUE in read.metharray
minfi
methylation
epic
6.8 years ago
jbar3141
• 0
0
votes
0
replies
1.4k
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi
methylation
EPIC
6.8 years ago
sichan
• 0
2
votes
3
replies
3.0k
views
"Seems your IDAT file not from one Array"
EPIC
methylation
ChAMP
updated 7.1 years ago by
yura.grabovska
▴ 30 • written 7.1 years ago by
david.ch
• 0
0
votes
2
replies
2.7k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 8.0 years ago by
Guido Hooiveld
★ 4.1k • written 8.0 years ago by
Ellen O
• 0
1
vote
3
replies
1.9k
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
2.5k
views
Unknown annotation in the RGChannelSetExtended object
minfi
idat
annotation
EPIC
updated 8.2 years ago by
xue.zhang
• 0 • written 8.2 years ago by
Frocha
▴ 20
0
votes
5
replies
2.7k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon
methylation
EPIC
normalization
8.4 years ago • updated 8.3 years ago
Wade Davis
▴ 60
0
votes
0
replies
1.7k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
8.6 years ago
Yuan Tian
▴ 90
0
votes
1
reply
2.4k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
8.7 years ago
Yuan Tian
▴ 90
1
vote
2
replies
2.0k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
8.9 years ago
m.van_iterson
▴ 20
0
votes
2
replies
1.5k
views
error using EPIC early access version arrays with minfi
epic
minfi
read.metharray
software error
8.9 years ago
mcastrod
• 0
29 results • Page
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Recent ...
Replies
Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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