Showing : methylation • reset
1
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591
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
12 weeks ago • updated 8 weeks ago Kim • 0
0
votes
1
reply
218
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 3 months ago by 66k • written 3 months ago by • 0
1
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8
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667
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
0
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323
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
6 months ago kyj2226 • 0
1
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3
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1.5k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 7 months ago by ▴ 730 • written 3.2 years ago by • 0
0
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7
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2.0k
views
error with champ.load
ChAMP champ methylation
updated 10 months ago by • 0 • written 4.2 years ago by • 0
0
votes
2
replies
830
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error in champ.SVD
svd methylation champ
updated 14 months ago by 3.9k • written 14 months ago by • 0
1
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0
replies
618
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
23 months ago hlee ▴ 10
2
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1
reply
691
views
Limma model orientation
limma methylation MethylationArray
updated 2.2 years ago by 66k • written 2.2 years ago by • 0
0
votes
2
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2.8k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.2 years ago by • 0 • written 8.8 years ago by ▴ 10
1
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1
reply
819
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.3 years ago by ▴ 90 • written 2.3 years ago by ▴ 10
0
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0
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761
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.4 years ago Lorenzo • 0
0
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1
reply
1.2k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.7 years ago by ▴ 10 • written 3.0 years ago by ▴ 80
2
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2
replies
909
views
How to overcome issue linked to loading big R object
minfi R methylation
3.2 years ago Federica ▴ 10
1
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5
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4.4k
views
minfi - error when reading idat files
minfi methylation
updated 21 months ago by • 0 • written 7.0 years ago by ▴ 10
0
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0
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1.0k
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.4 years ago epibio ▴ 10
0
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1
reply
903
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 20
0
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0
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778
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
3.9 years ago i.s.castanho • 0
0
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1
reply
671
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.1 years ago AishaD • 0
2
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1
reply
1.1k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.2 years ago Zach Roe ▴ 10
0
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0
replies
927
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.2 years ago marcin.bazyliszek • 0
0
votes
1
reply
640
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.3 years ago i.s.castanho • 0
1
vote
1
reply
986
views
SVA paired samples
SVA EPIC methylation limma
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
0
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4
replies
951
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.4 years ago i.s.brorson • 0
1
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3
replies
1.5k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.4 years ago erwin.tomasich ▴ 10
1
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1
reply
852
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.4 years ago by ▴ 90 • written 4.5 years ago by • 0
0
votes
0
replies
745
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.5 years ago A ▴ 40
0
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1
reply
2.8k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
4.5 years ago ph.shimaasherif • 0
2
votes
16
replies
2.7k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 20
0
votes
8
replies
1.1k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.5 years ago sara.blocquiaux • 0
0
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0
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706
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
4.5 years ago luciomora8 • 0
0
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1
reply
1.0k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 4.6 years ago by ★ 3.9k • written 4.6 years ago by • 0
1
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3
replies
1.1k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
1
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3
replies
1.1k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.7 years ago patriciasolesanchez • 0
0
votes
1
reply
728
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
4.7 years ago sorjuelal • 0
0
votes
2
replies
899
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 4.7 years ago by 66k • written 4.7 years ago by • 0
3
votes
5
replies
1.5k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.7 years ago by 66k • written 4.7 years ago by ▴ 10
0
votes
0
replies
762
views
DSS for non-CpG site analysis
DSS methylation
4.8 years ago CalM • 0
0
votes
4
replies
1.7k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 17 months ago by • 0 • written 4.8 years ago by • 0
1
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3
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1.5k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.8 years ago by ▴ 10 • written 4.8 years ago by • 0
1
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6
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1.8k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.8 years ago sabrina.mcnew • 0
1
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2
replies
3.8k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.2 years ago by • 0 • written 5.2 years ago by • 0
1
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4
replies
1.6k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 5.0 years ago by ▴ 60 • written 5.0 years ago by • 0
0
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2
replies
2.1k
views
ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP methylation BMIQ
updated 7 months ago by • 0 • written 5.2 years ago by ▴ 20
0
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0
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1.3k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.2 years ago gerald.mccollam • 0
4
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4
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1.3k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.3 years ago by ★ 6.5k • written 5.3 years ago by • 0
0
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0
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1.2k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
5.4 years ago • updated 5.3 years ago moldach ▴ 20
0
votes
1
reply
970
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.5 years ago by 66k • written 5.5 years ago by • 0
1
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2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.5 years ago by ★ 1.3k • written 5.6 years ago by • 0
2
votes
1
reply
1.4k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 5.6 years ago by ▴ 290 • written 5.6 years ago by ▴ 10
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Comment: Epicv2 conversion fail by Alex • 0
Thank you for your support. > In the double conversion, the output you supplied indicates that the number of probes is the same (453093)? …
Comment: OST to PST Converter Software by Deepak • 0
One can also check out a professional solution named Weeom OST to PST Converter Software. It is a reliable and secure solution to repair co…
Comment: How to search Pubmed Central or other fulltext literature base using regex? by Abiologist • 0
Apologies - you are potentially correct (assuming there is no answer within Bioconductor). I'm having trouble finding a suitable venue for …
Comment: How to search Pubmed Central or other fulltext literature base using regex? by ATpoint ★ 4.2k
This is off-topic as entirely unrelated to Bioconductor. You seem to be crossposting this to > 1 community, please at least leave a link to…
Comment: Struggling to convert a large list of non-model genes into human orthologs, any by ronin • 0
Thank you very much for your detailed reply, this was a big help. Just in case others come across this problem in the future, the code did …
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C: ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Help with error running DiffBind
Comment: Difference between enrichGO results and Enrichr website results
A: Unable to install the package "tissuesGeneExpression"
Unable to install the package "tissuesGeneExpression"
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