Showing : Methylation • reset
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 10
1
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2
replies
531
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
3 months ago ramiro.barrantes ▴ 10
1
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3
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1.8k
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 12 weeks ago by • 0 • written 9 months ago by • 0
0
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1
reply
531
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 9 months ago by 67k • written 9 months ago by • 0
1
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8
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1.0k
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 11 months ago by 52k • written 11 months ago by • 0
0
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0
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659
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
12 months ago kyj2226 • 0
1
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3
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2.0k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 13 months ago by ▴ 750 • written 3.7 years ago by • 0
0
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7
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2.3k
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error with champ.load
ChAMP champ methylation
updated 16 months ago by • 0 • written 4.7 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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775
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.5 years ago hlee ▴ 10
2
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1
reply
859
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 2.7 years ago by • 0 • written 9.3 years ago by ▴ 10
1
vote
1
reply
969
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.8 years ago by ▴ 100 • written 2.8 years ago by ▴ 10
0
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0
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909
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.9 years ago Lorenzo • 0
0
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1
reply
1.7k
views
Gene level methylation values
methylation methylKit bsseq
updated 3.2 years ago by ▴ 10 • written 3.5 years ago by ▴ 80
2
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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
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4.9k
views
minfi - error when reading idat files
minfi methylation
updated 2.3 years ago by • 0 • written 7.5 years ago by ▴ 10
0
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0
replies
1.1k
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 4.4 years ago by ★ 4.0k • written 4.4 years ago by ▴ 20
0
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0
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922
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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
816
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.6 years ago AishaD • 0
2
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1
reply
1.2k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.7 years ago Zach Roe ▴ 10
0
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0
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1.1k
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.7 years ago marcin.bazyliszek • 0
0
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1
reply
771
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.8 years ago i.s.castanho • 0
1
vote
1
reply
1.2k
views
SVA paired samples
SVA EPIC methylation limma
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
0
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4
replies
1.2k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.9 years ago i.s.brorson • 0
1
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3
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1.7k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.9 years ago erwin.tomasich ▴ 10
1
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1
reply
991
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
900
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
5.0 years ago ph.shimaasherif • 0
2
votes
16
replies
3.3k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.0 years ago by ▴ 290 • written 5.0 years ago by ▴ 20
0
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8
replies
1.3k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.0 years ago sara.blocquiaux • 0
0
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0
replies
840
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Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.0 years ago luciomora8 • 0
0
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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 5.1 years ago by • 0
1
vote
3
replies
1.3k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 5.1 years ago by 67k • written 5.1 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
878
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
5.2 years ago sorjuelal • 0
0
votes
2
replies
1.0k
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 5.2 years ago by 67k • written 5.2 years ago by • 0
3
votes
5
replies
1.7k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 10
0
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0
replies
907
views
DSS for non-CpG site analysis
DSS methylation
5.3 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 23 months ago by • 0 • written 5.4 years ago by • 0
1
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3
replies
1.8k
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
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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
4.3k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.7 years ago by • 0 • written 5.7 years ago by • 0
1
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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
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4
replies
1.5k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.8 years ago by ★ 6.5k • written 5.8 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
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: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.
Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k
You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
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Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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