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EPIC
•
reset
0
votes
0
replies
435
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
12 months ago
Jitendra
▴ 10
0
votes
2
replies
989
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
3.9 years ago • updated 3.4 years ago
Nala
• 0
2
votes
1
reply
934
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
3.9 years ago
Zach Roe
▴ 10
1
vote
1
reply
905
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
whyw6948
• 0
1
vote
3
replies
1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.1 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
783
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 4.2 years ago by
Yuan Tian
▴ 90 • written 4.2 years ago by
cherlyn.t
• 0
2
votes
16
replies
2.4k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 4.2 years ago by
Yuan Tian
▴ 270 • written 4.2 years ago by
Ankit
▴ 20
3
votes
5
replies
1.3k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
yoursbassanio
▴ 10
0
votes
4
replies
1.5k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 14 months ago by
shuo
• 0 • written 4.6 years ago by
enora.fremy
• 0
0
votes
1
reply
1.7k
views
How to analyse 450k and EPIC methylation data together?
minfi
450k
EPIC
analysis
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
maduran
• 0
0
votes
3
replies
1.2k
views
Limma for cell components effect on response
450k
EPIC
minfi
limma
cell components
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
antgomo
• 0
1
vote
3
replies
1.2k
views
Obtaining annotated results from rnbeads
rnbeads
EPIC
updated 4.8 years ago by
mscherer
▴ 50 • written 4.8 years ago by
Mark Dunning
★ 1.1k
0
votes
0
replies
1.0k
views
Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
5.0 years ago
rmf
▴ 20
0
votes
0
replies
800
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
5.0 years ago
rmf
▴ 20
2
votes
1
reply
1.2k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 5.3 years ago by
Yuan Tian
▴ 270 • written 5.3 years ago by
D
▴ 10
0
votes
2
replies
2.0k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP
Normalization
FunctionalNormalization
methylation
EPIC
5.5 years ago
yuabrahamliu
• 0
5
votes
9
replies
1.6k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
c.bettencourt
• 0
0
votes
0
replies
865
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
5.6 years ago
peter.fransquet
• 0
0
votes
3
replies
1.5k
views
Minfi error when using force=TRUE in read.metharray
minfi
methylation
epic
5.6 years ago
jbar3141
• 0
0
votes
0
replies
1.1k
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi
methylation
EPIC
5.7 years ago
sichan
• 0
2
votes
3
replies
2.0k
views
"Seems your IDAT file not from one Array"
EPIC
methylation
ChAMP
updated 6.0 years ago by
yura.grabovska
▴ 30 • written 6.0 years ago by
david.ch
• 0
0
votes
2
replies
1.8k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 6.9 years ago by
Guido Hooiveld
★ 3.9k • written 6.9 years ago by
Ellen O
• 0
1
vote
3
replies
1.5k
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
1.9k
views
Unknown annotation in the RGChannelSetExtended object
minfi
idat
annotation
EPIC
updated 7.0 years ago by
xue.zhang
• 0 • written 7.1 years ago by
Frocha
▴ 20
0
votes
5
replies
2.1k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon
methylation
EPIC
normalization
7.2 years ago
Wade Davis
▴ 60
0
votes
0
replies
1.3k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
7.5 years ago
Yuan Tian
▴ 90
0
votes
1
reply
1.9k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
7.6 years ago
Yuan Tian
▴ 90
1
vote
2
replies
1.6k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
7.7 years ago
m.van_iterson
▴ 20
0
votes
2
replies
1.2k
views
error using EPIC early access version arrays with minfi
epic
minfi
read.metharray
software error
7.8 years ago
mcastrod
• 0
29 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
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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