Showing : Methylation • reset
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218
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 23 days ago by ▴ 170 • written 23 days ago by • 0
0
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1
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145
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 25 days ago by 65k • written 26 days ago by • 0
1
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8
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530
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 3 months ago by • 0
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0
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246
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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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743
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error in champ.SVD
svd methylation champ
updated 12 months ago by 3.8k • written 12 months ago by • 0
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564
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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
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649
views
Limma model orientation
limma methylation MethylationArray
updated 24 months ago by 65k • written 24 months ago by • 0
1
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1
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777
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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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723
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WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.2 years ago Lorenzo • 0
0
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1
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1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.5 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
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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
2
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2
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860
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How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
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0
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960
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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
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1
reply
856
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 3.8 years ago by ▴ 20
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746
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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
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1
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637
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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
978
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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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874
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.0 years ago marcin.bazyliszek • 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 4.0 years ago by • 0
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1
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605
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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
942
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SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
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4
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903
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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
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1.4k
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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
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819
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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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692
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
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0
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671
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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
967
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
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3
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1.0k
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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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689
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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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850
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
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5
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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
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0
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726
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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1.4k
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
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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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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
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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
5.1 years ago gerald.mccollam • 0
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4
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1.3k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.1 years ago by ★ 6.5k • written 5.2 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
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1
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917
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
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1.4k
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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
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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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813
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
5.5 years ago saripalligautam86 ▴ 10
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2
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2.1k
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ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
5.6 years ago yuabrahamliu • 0
50 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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