Showing : Methylation • reset
0
votes
2
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177
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error in champ.SVD
svd methylation champ
updated 7 weeks ago by 3.5k • written 7 weeks ago by • 0
1
vote
0
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231
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
10 months ago hlee ▴ 10
2
votes
1
reply
359
views
Limma model orientation
limma methylation MethylationArray
updated 13 months ago by 63k • written 13 months ago by • 0
0
votes
2
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2.1k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 13 months ago by • 0 • written 7.7 years ago by ▴ 10
1
vote
1
reply
413
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 15 months ago by ▴ 90 • written 15 months ago by ▴ 10
0
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0
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396
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WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
16 months ago Lorenzo • 0
0
votes
1
reply
556
views
Gene level methylation values
methylation methylKit bsseq
updated 20 months ago by ▴ 10 • written 23 months ago by ▴ 80
1
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1
reply
643
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 2.1 years ago by ▴ 730 • written 2.1 years ago by • 0
2
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2
replies
554
views
How to overcome issue linked to loading big R object
minfi R methylation
2.1 years ago Federica ▴ 10
1
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5
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3.0k
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minfi - error when reading idat files
minfi methylation
updated 8 months ago by • 0 • written 5.9 years ago by ▴ 10
0
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0
replies
658
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
2.4 years ago epibio ▴ 10
0
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1
reply
555
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 2.8 years ago by 3.8k • written 2.9 years ago by ▴ 20
0
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0
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423
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
2.9 years ago i.s.castanho • 0
0
votes
1
reply
377
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
3.1 years ago AishaD • 0
2
votes
1
reply
656
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
3.1 years ago Zach Roe ▴ 10
0
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0
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557
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
3.1 years ago marcin.bazyliszek • 0
0
votes
6
replies
983
views
error with champ.load
ChAMP champ methylation
updated 22 months ago by • 0 • written 3.2 years ago by • 0
0
votes
1
reply
364
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
3.2 years ago i.s.castanho • 0
1
vote
1
reply
598
views
SVA paired samples
SVA EPIC methylation limma
updated 3.3 years ago by 63k • written 3.3 years ago by • 0
0
votes
4
replies
554
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
3.3 years ago i.s.brorson • 0
1
vote
3
replies
915
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
3.4 years ago erwin.tomasich ▴ 10
1
vote
1
reply
581
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 3.4 years ago by ▴ 90 • written 3.4 years ago by • 0
0
votes
0
replies
414
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
3.4 years ago A ▴ 40
0
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1
reply
2.1k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
3.4 years ago ph.shimaasherif • 0
2
votes
16
replies
1.6k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 3.4 years ago by ▴ 270 • written 3.4 years ago by ▴ 20
0
votes
8
replies
629
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
3.4 years ago sara.blocquiaux • 0
0
votes
0
replies
437
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
3.4 years ago luciomora8 • 0
0
votes
1
reply
616
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 3.5 years ago by 3.8k • written 3.5 years ago by • 0
1
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3
replies
667
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 3.5 years ago by 63k • written 3.6 years ago by • 0
1
vote
3
replies
646
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
3.6 years ago patriciasolesanchez • 0
0
votes
1
reply
437
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
3.6 years ago sorjuelal • 0
0
votes
2
replies
594
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 3.7 years ago by 63k • written 3.7 years ago by • 0
3
votes
5
replies
848
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 3.7 years ago by 63k • written 3.7 years ago by ▴ 10
0
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0
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429
views
DSS for non-CpG site analysis
DSS methylation
3.7 years ago CalM • 0
0
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4
replies
1.0k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 4 months ago by • 0 • written 3.8 years ago by • 0
1
vote
3
replies
1.0k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 3.8 years ago by ▴ 10 • written 3.8 years ago by • 0
1
vote
6
replies
1.0k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
3.8 years ago sabrina.mcnew • 0
1
vote
2
replies
2.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 2.1 years ago by • 0 • written 4.1 years ago by • 0
1
vote
4
replies
997
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.0 years ago by ▴ 60 • written 4.0 years ago by • 0
0
votes
1
reply
1.4k
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 4.1 years ago by ▴ 270 • written 4.1 years ago by ▴ 20
0
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0
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940
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
4.2 years ago gerald.mccollam • 0
4
votes
4
replies
837
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 4.2 years ago by 6.5k • written 4.3 years ago by • 0
0
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0
replies
812
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
4.3 years ago moldach ▴ 20
0
votes
1
reply
639
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 4.4 years ago by 63k • written 4.4 years ago by • 0
1
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2
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1.0k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by • 0
2
votes
1
reply
914
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 4.5 years ago by ▴ 270 • written 4.5 years ago by • 0
0
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0
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543
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
4.6 years ago saripalligautam86 ▴ 10
0
votes
2
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1.6k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
4.7 years ago yuabrahamliu • 0
1
vote
2
replies
1.6k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 4.7 years ago by 63k • written 4.7 years ago by ▴ 20
2
votes
8
replies
1.3k
views
edgeR: design matrix for methylation analysis
edger methylation
updated 4.7 years ago by 47k • written 4.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
Votes
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
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