Showing : methylation • reset
1
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2
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281
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 22 hours ago Kim • 0
0
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1
reply
159
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
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8
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544
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
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0
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256
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
1
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3
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1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
0
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7
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1.8k
views
error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.1 years ago by • 0
0
votes
2
replies
753
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error in champ.SVD
svd methylation champ
updated 12 months ago by 3.9k • written 12 months ago by • 0
1
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0
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572
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
2
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1
reply
656
views
Limma model orientation
limma methylation MethylationArray
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
0
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2
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2.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.0 years ago by • 0 • written 8.6 years ago by ▴ 10
1
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1
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782
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.2 years ago by ▴ 90 • written 2.2 years ago by ▴ 10
0
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0
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730
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.3 years ago Lorenzo • 0
0
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1
reply
1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.6 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
2
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2
replies
871
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
1
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5
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4.1k
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minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
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0
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969
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
0
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1
reply
864
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by ▴ 20
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0
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751
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
3.8 years ago i.s.castanho • 0
0
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1
reply
644
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.0 years ago AishaD • 0
2
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1
reply
990
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
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0
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880
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.1 years ago marcin.bazyliszek • 0
0
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1
reply
610
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
1
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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
0
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4
replies
913
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Fix regions for bumphunter
bumphunter DMR methylation minfi
4.2 years ago i.s.brorson • 0
1
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3
replies
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.3 years ago erwin.tomasich ▴ 10
1
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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
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0
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702
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.3 years ago A ▴ 40
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1
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2.7k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
4.3 years ago ph.shimaasherif • 0
2
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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
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8
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1.0k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.3 years ago sara.blocquiaux • 0
0
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0
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674
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
4.3 years ago luciomora8 • 0
0
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1
reply
976
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 4.4 years ago by ★ 3.9k • written 4.4 years ago by • 0
1
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3
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1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
1
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3
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1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.5 years ago patriciasolesanchez • 0
0
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1
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695
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Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
4.5 years ago sorjuelal • 0
0
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2
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857
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
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
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0
replies
728
views
DSS for non-CpG site analysis
DSS methylation
4.6 years ago CalM • 0
0
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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
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 4.7 years ago by ▴ 10 • written 4.7 years ago by • 0
1
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6
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1.7k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.7 years ago sabrina.mcnew • 0
1
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2
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3.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.0 years ago by • 0 • written 5.0 years ago by • 0
1
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4
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1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.9 years ago by ▴ 60 • written 4.9 years ago by • 0
0
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2
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2.0k
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 5 months ago by • 0 • written 5.0 years ago by ▴ 20
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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
5.1 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 5.2 years ago by ★ 6.5k • written 5.2 years ago by • 0
0
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0
replies
1.1k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
5.2 years ago moldach ▴ 20
0
votes
1
reply
924
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.3 years ago by 65k • written 5.3 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 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
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
50 results • Page 1 of 1
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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: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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