Showing : methylation • reset
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191
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 15 days ago by ▴ 170 • written 16 days ago by • 0
0
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1
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128
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 17 days ago by 65k • written 19 days ago by • 0
1
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8
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510
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
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0
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233
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
0
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2
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729
views
error in champ.SVD
svd methylation champ
updated 12 months ago by 3.8k • written 12 months ago by • 0
1
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0
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548
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
21 months ago hlee ▴ 10
2
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1
reply
643
views
Limma model orientation
limma methylation MethylationArray
updated 23 months ago by 65k • written 23 months ago by • 0
1
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1
reply
771
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by ▴ 10
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0
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716
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.2 years ago Lorenzo • 0
0
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1
reply
1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.5 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
1
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3
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1.3k
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
2
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2
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851
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
0
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0
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951
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.2 years ago epibio ▴ 10
0
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1
reply
847
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 20
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0
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740
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
3.7 years ago i.s.castanho • 0
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1
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623
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
3.9 years ago AishaD • 0
2
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1
reply
969
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
0
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0
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865
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.0 years ago marcin.bazyliszek • 0
0
votes
7
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1.8k
views
error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.0 years ago by • 0
0
votes
1
reply
599
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
1
vote
1
reply
932
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
0
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4
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896
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.2 years ago i.s.brorson • 0
1
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3
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1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.2 years ago erwin.tomasich ▴ 10
1
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1
reply
807
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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684
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
replies
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 ▴ 270 • written 4.3 years ago by ▴ 20
0
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8
replies
997
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.3 years ago sara.blocquiaux • 0
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0
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665
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
956
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 4.4 years ago by 65k • written 4.4 years ago by • 0
1
vote
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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673
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
4.5 years ago sorjuelal • 0
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2
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836
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 4.5 years ago by 65k • written 4.5 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 4.5 years ago by ▴ 10
0
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0
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717
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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1.5k
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 4.6 years ago by • 0
1
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3
replies
1.4k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
1
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6
replies
1.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.7 years ago sabrina.mcnew • 0
1
vote
4
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1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.8 years ago by ▴ 60 • written 4.8 years ago by • 0
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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
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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
5.0 years ago gerald.mccollam • 0
4
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4
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1.2k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.1 years ago by ★ 6.5k • written 5.1 years ago by • 0
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0
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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
907
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
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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 ▴ 270 • written 5.4 years ago by ▴ 10
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0
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807
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
5.4 years ago saripalligautam86 ▴ 10
0
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2
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2.1k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
5.5 years ago yuabrahamliu • 0
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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