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Epic
•
reset
0
votes
0
replies
735
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
2.1 years ago
Jitendra
▴ 10
0
votes
2
replies
1.4k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
5.0 years ago • updated 4.5 years ago
Nala
• 0
2
votes
1
reply
1.3k
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
5.0 years ago
Zach Roe
▴ 10
1
vote
1
reply
1.3k
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
whyw6948
• 0
1
vote
3
replies
1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.2 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 5.3 years ago by
Yuan Tian
▴ 290 • written 5.3 years ago by
Ankit
▴ 20
3
votes
5
replies
1.8k
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
2.2k
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
2.5k
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 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 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 5.9 years ago by
Mark Dunning
★ 1.1k
0
votes
0
replies
1.4k
views
Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
6.1 years ago
firestar
▴ 20
0
votes
0
replies
1.0k
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
6.1 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 6.4 years ago by
Yuan Tian
▴ 290 • written 6.4 years ago by
D
▴ 10
0
votes
2
replies
2.6k
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 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 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
6.7 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
2.6k
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 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
2.5k
views
Unknown annotation in the RGChannelSetExtended object
minfi
idat
annotation
EPIC
updated 8.1 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
8.3 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
1.9k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
8.8 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
1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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