Showing : Methylation • reset
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5
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2.2k
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Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
written 8.8 years ago by • 0
0
votes
13
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1.6k
views
When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 8 months ago by ▴ 20 • written 8 months ago by ▴ 10
1
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2
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897
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
8 months ago ramiro.barrantes ▴ 10
1
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3
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2.6k
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 7 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
751
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 13 months ago by 68k • written 13 months ago by • 0
1
vote
8
replies
1.3k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 15 months ago by 52k • written 16 months ago by • 0
0
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0
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977
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
17 months ago kyj2226 • 0
1
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3
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2.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 18 months ago by ▴ 750 • written 4.0 years ago by • 0
0
votes
7
replies
2.5k
views
error with champ.load
ChAMP champ methylation
updated 21 months ago by • 0 • written 5.1 years ago by • 0
0
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2
replies
1.2k
views
error in champ.SVD
svd methylation champ
updated 2.1 years ago by 4.1k • written 2.1 years ago by • 0
1
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0
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866
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.9 years ago hlee ▴ 10
2
votes
1
reply
954
views
Limma model orientation
limma methylation MethylationArray
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
2
replies
3.4k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.1 years ago by • 0 • written 9.6 years ago by ▴ 10
1
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1
reply
1.1k
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.2 years ago by ▴ 100 • written 3.2 years ago by ▴ 10
0
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0
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985
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.3 years ago Lorenzo • 0
0
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1
reply
2.2k
views
Gene level methylation values
methylation methylKit bsseq
updated 3.6 years ago by ▴ 10 • written 3.9 years ago by ▴ 80
2
votes
2
replies
1.2k
views
How to overcome issue linked to loading big R object
minfi R methylation
4.0 years ago Federica ▴ 10
1
vote
5
replies
5.3k
views
minfi - error when reading idat files
minfi methylation
updated 2.7 years ago by • 0 • written 7.9 years ago by ▴ 10
0
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0
replies
1.3k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.3 years ago epibio ▴ 10
0
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1
reply
1.2k
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 20
0
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0
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997
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.8 years ago i.s.castanho • 0
0
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1
reply
918
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
5.0 years ago AishaD • 0
2
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1
reply
1.3k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
5.1 years ago Zach Roe ▴ 10
0
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0
replies
1.2k
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
5.1 years ago marcin.bazyliszek • 0
0
votes
1
reply
859
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.2 years ago i.s.castanho • 0
1
vote
1
reply
1.3k
views
SVA paired samples
SVA EPIC methylation limma
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
4
replies
1.3k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.3 years ago i.s.brorson • 0
1
vote
3
replies
1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.3 years ago erwin.tomasich ▴ 10
1
vote
1
reply
1.1k
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 5.3 years ago by ▴ 90 • written 5.3 years ago by • 0
0
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0
replies
978
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.4 years ago A ▴ 60
0
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1
reply
3.4k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
5.4 years ago ph.shimaasherif • 0
2
votes
16
replies
3.8k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.4 years ago by ▴ 290 • written 5.4 years ago by ▴ 20
0
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8
replies
1.4k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.4 years ago sara.blocquiaux • 0
0
votes
0
replies
916
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.4 years ago luciomora8 • 0
0
votes
1
reply
1.5k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.4 years ago by ★ 4.0k • written 5.5 years ago by • 0
1
vote
3
replies
1.5k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
1
vote
3
replies
1.5k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
5.5 years ago patriciasolesanchez • 0
0
votes
1
reply
993
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
5.6 years ago sorjuelal • 0
0
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2
replies
1.1k
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
3
votes
5
replies
1.9k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 10
0
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0
replies
1.0k
views
DSS for non-CpG site analysis
DSS methylation
5.7 years ago CalM • 0
0
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4
replies
2.3k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 2.3 years ago by • 0 • written 5.7 years ago by • 0
1
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3
replies
2.0k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 5.7 years ago by ▴ 10 • written 5.7 years ago by • 0
1
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6
replies
2.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
5.7 years ago sabrina.mcnew • 0
1
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2
replies
4.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 4.1 years ago by • 0 • written 6.0 years ago by • 0
1
vote
4
replies
2.2k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 5.9 years ago by ▴ 60 • written 5.9 years ago by • 0
0
votes
2
replies
2.7k
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 18 months ago by • 0 • written 6.0 years ago by ▴ 20
0
votes
0
replies
1.5k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
6.1 years ago gerald.mccollam • 0
4
votes
4
replies
1.7k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 6.2 years ago by ★ 6.5k • written 6.2 years ago by • 0
0
votes
0
replies
1.5k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.3 years ago • updated 6.2 years ago moldach ▴ 20
50 results • Page 1 of 1
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Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your explanation, that makes sense. Do you have any suggestions on how to deal with this issue? if it is an issue? especially…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by nytwordlehints • 0
I have always had a great fondness for games, so witnessing their transformation into animated versions is truly a delightful experience. […
Comment: FlowSOM is unable to create Output by EvangelinePope • 0
I will remember it, Thank you so much for sharing.
Answer: Limma suqeezeVar by Gordon Smyth 52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
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Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
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