Showing : EPIC • reset
2
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16
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2.5k
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Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by ▴ 20
5
votes
9
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1.7k
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 5.6 years ago by ★ 28k • written 5.7 years ago by • 0
0
votes
5
replies
2.2k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
7.3 years ago Wade Davis ▴ 60
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.6 years ago by 65k • written 4.6 years ago by ▴ 10
0
votes
4
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1.6k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 15 months ago by • 0 • written 4.7 years ago by • 0
1
vote
3
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1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.3 years ago erwin.tomasich ▴ 10
0
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3
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1.6k
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
5.7 years ago jbar3141 • 0
2
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3
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2.1k
views
"Seems your IDAT file not from one Array"
EPIC methylation ChAMP
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
0
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3
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1.2k
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
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3
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2.0k
views
Unknown annotation in the RGChannelSetExtended object
minfi idat annotation EPIC
updated 7.1 years ago by • 0 • written 7.2 years ago by ▴ 20
1
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3
replies
1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
1
vote
3
replies
1.2k
views
Obtaining annotated results from rnbeads
rnbeads EPIC
updated 4.9 years ago by ▴ 50 • written 4.9 years ago by ★ 1.1k
0
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2
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1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 7.0 years ago by ★ 3.9k • written 7.0 years ago by • 0
0
votes
2
replies
2.1k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
5.6 years ago yuabrahamliu • 0
0
votes
2
replies
1.2k
views
error using EPIC early access version arrays with minfi
epic minfi read.metharray software error
7.9 years ago mcastrod • 0
0
votes
2
replies
1.0k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
4.1 years ago • updated 3.5 years ago Nala • 0
1
vote
2
replies
1.6k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi illuminaio epic
7.8 years ago m.van_iterson ▴ 20
2
votes
1
reply
1.3k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 5.4 years ago by ▴ 280 • written 5.4 years ago by ▴ 10
0
votes
1
reply
2.0k
views
News: Bug in ChAMP package champ.SVD() function
champ methylation 450k SVD EPIC News
7.7 years ago Yuan Tian ▴ 90
0
votes
1
reply
1.8k
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 4.7 years ago by 65k • written 4.7 years ago by • 0
1
vote
1
reply
824
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by • 0
1
vote
1
reply
947
views
SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
2
votes
1
reply
988
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
0
votes
0
replies
1.4k
views
News: ChAMP2 is online
epigenetics EPIC 450K ChAMP News
7.6 years ago Yuan Tian ▴ 90
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
5.8 years ago sichan • 0
0
votes
0
replies
483
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
13 months ago Jitendra ▴ 10
0
votes
0
replies
825
views
Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
5.1 years ago rmf ▴ 20
0
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0
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1.1k
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
5.1 years ago rmf ▴ 20
0
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0
replies
910
views
missMethyl EPIC manifest update
missmethyl epic illuminahumanmethylationepicanno.ilm10b4.hg19. ruv
5.7 years ago peter.fransquet • 0
29 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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