Showing : epic • reset
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5
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2.2k
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Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
7.3 years ago Wade Davis ▴ 60
1
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2
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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
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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
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
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2
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1.2k
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error using EPIC early access version arrays with minfi
epic minfi read.metharray software error
7.9 years ago mcastrod • 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
2
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1
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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
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1
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2.0k
views
News: Bug in ChAMP package champ.SVD() function
champ methylation 450k SVD EPIC News
7.7 years ago Yuan Tian ▴ 90
1
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3
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1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
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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
5
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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 5.6 years ago by • 0
1
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3
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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
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3
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1.2k
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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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1
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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
3
votes
5
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1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.5 years ago by 65k • written 4.6 years ago by ▴ 10
2
votes
16
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2.5k
views
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
1
vote
1
reply
813
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
939
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
2
votes
1
reply
973
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
0
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2
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1.0k
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Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
4.0 years ago • updated 3.5 years ago Nala • 0
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
0
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0
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896
views
missMethyl EPIC manifest update
missmethyl epic illuminahumanmethylationepicanno.ilm10b4.hg19. ruv
5.7 years ago peter.fransquet • 0
0
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0
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1.4k
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News: ChAMP2 is online
epigenetics EPIC 450K ChAMP News
7.6 years ago Yuan Tian ▴ 90
0
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2
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2.1k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
5.6 years ago yuabrahamliu • 0
0
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0
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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
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0
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1.0k
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
5.1 years ago rmf ▴ 20
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0
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819
views
Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
5.1 years ago rmf ▴ 20
1
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3
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1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.2 years ago erwin.tomasich ▴ 10
0
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0
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471
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
13 months ago Jitendra ▴ 10
29 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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