Showing : methylation • reset
0
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13
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984
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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
vote
2
replies
509
views
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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1.7k
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 10 weeks ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
514
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 8 months ago by 67k • written 8 months ago by • 0
1
vote
8
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1.0k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 10 months ago by 52k • written 11 months ago by • 0
0
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0
replies
643
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
12 months ago kyj2226 • 0
1
vote
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 3.6 years ago by • 0
0
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7
replies
2.3k
views
error with champ.load
ChAMP champ methylation
updated 16 months ago by • 0 • written 4.7 years ago by • 0
0
votes
2
replies
1.0k
views
error in champ.SVD
svd methylation champ
updated 20 months ago by 4.1k • written 20 months ago by • 0
1
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0
replies
770
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.4 years ago hlee ▴ 10
2
votes
1
reply
855
views
Limma model orientation
limma methylation MethylationArray
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
0
votes
2
replies
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 9.2 years ago by ▴ 10
1
vote
1
reply
957
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
votes
0
replies
901
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.9 years ago Lorenzo • 0
0
votes
1
reply
1.7k
views
Gene level methylation values
methylation methylKit bsseq
updated 3.2 years ago by ▴ 10 • written 3.4 years ago by ▴ 80
2
votes
2
replies
1.1k
views
How to overcome issue linked to loading big R object
minfi R methylation
3.6 years ago Federica ▴ 10
1
vote
5
replies
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
votes
0
replies
1.1k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.9 years ago epibio ▴ 10
0
votes
1
reply
1.0k
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
votes
0
replies
914
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.4 years ago i.s.castanho • 0
0
votes
1
reply
811
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.6 years ago AishaD • 0
2
votes
1
reply
1.2k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.7 years ago Zach Roe ▴ 10
0
votes
0
replies
1.1k
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.7 years ago marcin.bazyliszek • 0
0
votes
1
reply
763
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.7 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
votes
4
replies
1.1k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.9 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
4.9 years ago erwin.tomasich ▴ 10
1
vote
1
reply
980
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.9 years ago by ▴ 90 • written 4.9 years ago by • 0
0
votes
0
replies
893
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.9 years ago A ▴ 40
0
votes
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
3.2k
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
votes
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
835
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.0 years ago luciomora8 • 0
0
votes
1
reply
1.2k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.0 years ago by ★ 4.0k • written 5.0 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
5.1 years ago patriciasolesanchez • 0
0
votes
1
reply
869
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
900
views
DSS for non-CpG site analysis
DSS methylation
5.3 years ago CalM • 0
0
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4
replies
1.9k
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 5.3 years ago by • 0
1
vote
3
replies
1.8k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by • 0
1
vote
6
replies
2.2k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
5.3 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 5.6 years ago by • 0
1
vote
4
replies
1.9k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 5.5 years ago by ▴ 60 • written 5.5 years ago by • 0
0
votes
2
replies
2.4k
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 13 months ago by • 0 • written 5.6 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
5.7 years ago gerald.mccollam • 0
4
votes
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
1.3k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
5.9 years ago • updated 5.8 years ago moldach ▴ 20
0
votes
1
reply
1.1k
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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