Showing : Methylation • reset
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13
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1.1k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 4 months ago by ▴ 20 • written 4 months ago by ▴ 10
1
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2
replies
587
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
4 months ago ramiro.barrantes ▴ 10
1
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3
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1.9k
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
570
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 10 months ago by 67k • written 10 months ago by • 0
1
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8
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1.1k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 months ago by 52k • written 12 months ago by • 0
0
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0
replies
715
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
13 months ago kyj2226 • 0
1
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3
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2.1k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 14 months ago by ▴ 750 • written 3.7 years ago by • 0
0
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7
replies
2.3k
views
error with champ.load
ChAMP champ methylation
updated 17 months ago by • 0 • written 4.8 years ago by • 0
0
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2
replies
1.1k
views
error in champ.SVD
svd methylation champ
updated 21 months ago by 4.1k • written 21 months ago by • 0
1
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0
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793
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.6 years ago hlee ▴ 10
2
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1
reply
877
views
Limma model orientation
limma methylation MethylationArray
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
0
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2
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3.2k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.8 years ago by • 0 • written 9.3 years ago by ▴ 10
1
vote
1
reply
985
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.9 years ago by ▴ 100 • written 2.9 years ago by ▴ 10
0
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0
replies
921
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.0 years ago Lorenzo • 0
0
votes
1
reply
1.8k
views
Gene level methylation values
methylation methylKit bsseq
updated 3.3 years ago by ▴ 10 • written 3.6 years ago by ▴ 80
2
votes
2
replies
1.1k
views
How to overcome issue linked to loading big R object
minfi R methylation
3.7 years ago Federica ▴ 10
1
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5
replies
5.0k
views
minfi - error when reading idat files
minfi methylation
updated 2.4 years ago by • 0 • written 7.6 years ago by ▴ 10
0
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0
replies
1.2k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.0 years ago epibio ▴ 10
0
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1
reply
1.1k
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 20
0
votes
0
replies
934
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.5 years ago i.s.castanho • 0
0
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1
reply
829
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.7 years ago AishaD • 0
2
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1
reply
1.3k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.8 years ago Zach Roe ▴ 10
0
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0
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1.1k
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.8 years ago marcin.bazyliszek • 0
0
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1
reply
783
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.9 years ago i.s.castanho • 0
1
vote
1
reply
1.2k
views
SVA paired samples
SVA EPIC methylation limma
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
0
votes
4
replies
1.2k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.0 years ago i.s.brorson • 0
1
vote
3
replies
1.7k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.0 years ago erwin.tomasich ▴ 10
1
vote
1
reply
1.0k
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 5.0 years ago by ▴ 90 • written 5.0 years ago by • 0
0
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0
replies
912
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.0 years ago A ▴ 40
0
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1
reply
3.2k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
5.1 years ago ph.shimaasherif • 0
2
votes
16
replies
3.4k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.1 years ago by ▴ 290 • written 5.1 years ago by ▴ 20
0
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8
replies
1.3k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.1 years ago sara.blocquiaux • 0
0
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0
replies
855
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.1 years ago luciomora8 • 0
0
votes
1
reply
1.3k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.1 years ago by ★ 4.0k • written 5.2 years ago by • 0
1
vote
3
replies
1.3k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 5.2 years ago by 67k • written 5.2 years ago by • 0
1
vote
3
replies
1.3k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
5.2 years ago patriciasolesanchez • 0
0
votes
1
reply
893
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
5.3 years ago sorjuelal • 0
0
votes
2
replies
1.0k
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
3
votes
5
replies
1.7k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.3 years ago by 67k • written 5.3 years ago by ▴ 10
0
votes
0
replies
924
views
DSS for non-CpG site analysis
DSS methylation
5.4 years ago CalM • 0
0
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4
replies
2.0k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 2.0 years ago by • 0 • written 5.4 years ago by • 0
1
vote
3
replies
1.9k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 5.4 years ago by ▴ 10 • written 5.4 years ago by • 0
1
vote
6
replies
2.3k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
5.4 years ago sabrina.mcnew • 0
1
vote
2
replies
4.4k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.8 years ago by • 0 • written 5.7 years ago by • 0
1
vote
4
replies
1.9k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 5.6 years ago by ▴ 60 • written 5.6 years ago by • 0
0
votes
2
replies
2.5k
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 14 months ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
0
replies
1.4k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.8 years ago gerald.mccollam • 0
4
votes
4
replies
1.6k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.9 years ago by ★ 6.5k • written 5.9 years ago by • 0
0
votes
0
replies
1.4k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.0 years ago • updated 5.9 years ago moldach ▴ 20
0
votes
1
reply
1.1k
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
50 results • Page 1 of 1
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Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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