Showing : Methylation • reset
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Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
written 8.7 years ago by • 0
0
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13
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1.6k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 7 months ago by ▴ 20 • written 7 months ago by ▴ 10
1
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2
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843
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
7 months ago ramiro.barrantes ▴ 10
1
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3
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2.5k
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 6 months ago by • 0 • written 12 months ago by • 0
0
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1
reply
711
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 12 months ago by 68k • written 13 months ago by • 0
1
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8
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1.2k
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 15 months ago by 52k • written 15 months ago by • 0
0
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0
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933
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
16 months ago kyj2226 • 0
1
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3
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2.3k
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Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 17 months ago by ▴ 750 • written 4.0 years ago by • 0
0
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7
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2.5k
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error with champ.load
ChAMP champ methylation
updated 20 months ago by • 0 • written 5.0 years ago by • 0
0
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2
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1.2k
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error in champ.SVD
svd methylation champ
updated 2.0 years ago by 4.1k • written 2.0 years ago by • 0
1
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0
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855
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.8 years ago hlee ▴ 10
2
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1
reply
939
views
Limma model orientation
limma methylation MethylationArray
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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2
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3.4k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.0 years ago by • 0 • written 9.6 years ago by ▴ 10
1
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1
reply
1.1k
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.1 years ago by ▴ 100 • written 3.1 years ago by ▴ 10
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0
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977
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WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.2 years ago Lorenzo • 0
0
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1
reply
2.1k
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Gene level methylation values
methylation methylKit bsseq
updated 3.5 years ago by ▴ 10 • written 3.8 years ago by ▴ 80
2
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2
replies
1.2k
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How to overcome issue linked to loading big R object
minfi R methylation
4.0 years ago Federica ▴ 10
1
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5
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5.2k
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minfi - error when reading idat files
minfi methylation
updated 2.6 years ago by • 0 • written 7.8 years ago by ▴ 10
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0
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1.2k
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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
1.1k
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how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 20
0
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0
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986
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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
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1
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901
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.9 years ago AishaD • 0
2
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1
reply
1.3k
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
5.0 years ago Zach Roe ▴ 10
0
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0
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1.2k
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
5.0 years ago marcin.bazyliszek • 0
0
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1
reply
843
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.1 years ago i.s.castanho • 0
1
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1
reply
1.3k
views
SVA paired samples
SVA EPIC methylation limma
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
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4
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1.3k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.2 years ago i.s.brorson • 0
1
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3
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1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.2 years ago erwin.tomasich ▴ 10
1
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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
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965
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.3 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
5.3 years ago ph.shimaasherif • 0
2
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16
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3.8k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.3 years ago by ▴ 290 • written 5.3 years ago by ▴ 20
0
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8
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1.4k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.3 years ago sara.blocquiaux • 0
0
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0
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906
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.3 years ago luciomora8 • 0
0
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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 5.4 years ago by • 0
1
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3
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1.5k
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Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
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3
replies
1.5k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
5.5 years ago patriciasolesanchez • 0
0
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1
reply
973
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Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
5.5 years ago sorjuelal • 0
0
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2
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1.1k
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
3
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5
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1.8k
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
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993
views
DSS for non-CpG site analysis
DSS methylation
5.6 years ago CalM • 0
0
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4
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2.2k
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
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2.0k
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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
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2.6k
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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
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4.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 4.0 years ago by • 0 • written 6.0 years ago by • 0
1
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4
replies
2.1k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 5.9 years ago by ▴ 60 • written 5.9 years ago by • 0
0
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2
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2.6k
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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 17 months ago by • 0 • written 6.0 years ago by ▴ 20
0
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0
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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
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1.7k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 6.1 years ago by ★ 6.5k • written 6.1 years ago by • 0
0
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0
replies
1.4k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.2 years ago moldach ▴ 20
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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