Showing : methylation • reset
0
votes
1
reply
40
views
meffil.snp.concordance
MethylationArray methylationArrayAnalysis MethylationArrayData meffil methylation
updated 8 hours ago by 65k • written 12 hours ago by • 0
1
vote
2
replies
310
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 4 days ago Kim • 0
0
votes
1
reply
162
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
vote
8
replies
551
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
replies
262
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
1
vote
3
replies
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
votes
7
replies
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
758
views
error in champ.SVD
svd methylation champ
updated 12 months ago by 3.9k • written 12 months ago by • 0
1
vote
0
replies
575
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
2
votes
1
reply
658
views
Limma model orientation
limma methylation MethylationArray
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
0
votes
2
replies
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
vote
1
reply
784
views
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
votes
0
replies
735
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.3 years ago Lorenzo • 0
0
votes
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
votes
2
replies
873
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
1
vote
5
replies
4.2k
views
minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
0
votes
0
replies
971
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
0
votes
1
reply
867
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
0
votes
0
replies
752
views
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
votes
1
reply
645
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.0 years ago AishaD • 0
2
votes
1
reply
992
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
0
votes
0
replies
881
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.1 years ago marcin.bazyliszek • 0
0
votes
1
reply
612
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
950
views
SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
4
replies
916
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.3 years ago • updated 4.2 years ago i.s.brorson • 0
1
vote
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
vote
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
0
votes
0
replies
704
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.3 years ago A ▴ 40
0
votes
1
reply
2.8k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
4.3 years ago ph.shimaasherif • 0
2
votes
16
replies
2.6k
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
0
votes
8
replies
1.0k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.3 years ago sara.blocquiaux • 0
0
votes
0
replies
676
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
4.3 years ago luciomora8 • 0
0
votes
1
reply
981
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
vote
3
replies
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
vote
3
replies
1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.5 years ago patriciasolesanchez • 0
0
votes
1
reply
698
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
0
votes
2
replies
858
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
votes
0
replies
731
views
DSS for non-CpG site analysis
DSS methylation
4.6 years ago CalM • 0
0
votes
4
replies
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
vote
3
replies
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
vote
6
replies
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
vote
2
replies
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
vote
4
replies
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
votes
2
replies
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 6 months ago by • 0 • written 5.0 years ago by ▴ 20
0
votes
0
replies
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
votes
4
replies
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
votes
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
927
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
1
vote
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Popular Question to priyanka.m • 0
Locations • All
EMBL Heidelberg, 1 minute ago
United States, 5 minutes ago
United States, 10 minutes ago
United States, 25 minutes ago
India, 29 minutes ago
Traffic: 690 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6