Showing : methylation • reset
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 15 days ago by ▴ 170 • written 15 days ago by • 0
0
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1
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126
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 16 days ago by 65k • written 18 days ago by • 0
1
vote
8
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510
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
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0
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230
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
1
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3
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1.3k
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Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
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2
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2.0k
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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 5 months ago by • 0 • written 5.0 years ago by ▴ 20
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7
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1.8k
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error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.0 years ago by • 0
0
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2
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1.4k
views
Error processing Infinium 450K Methylation data using Minfi
minfi software error methylation illumina450k
updated 11 months ago by • 0 • written 8.3 years ago by • 0
1
vote
8
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3.3k
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Normalization starting from beta values in minfi
methylation minfi
written 7.9 years ago by ▴ 290
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2
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729
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error in champ.SVD
svd methylation champ
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
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4
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1.5k
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 4.6 years ago by • 0
1
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5
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4.1k
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minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
1
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0
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548
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
21 months ago hlee ▴ 10
1
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9
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3.6k
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strange results from differential methylation analysis using limma
limma methylation methyanalysis IMA
updated 23 months ago by 21k • written 7.1 years ago by • 0
2
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1
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642
views
Limma model orientation
limma methylation MethylationArray
updated 23 months ago by 65k • written 23 months ago by • 0
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2
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2.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 24 months ago by • 0 • written 8.6 years ago by ▴ 10
1
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1
reply
771
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by ▴ 10
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0
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716
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.2 years ago Lorenzo • 0
0
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1
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1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.5 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
2
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2
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850
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How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
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2
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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
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0
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950
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.2 years ago epibio ▴ 10
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1
reply
847
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 20
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0
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740
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
3.7 years ago i.s.castanho • 0
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1
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623
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
3.9 years ago AishaD • 0
2
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1
reply
969
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
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0
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864
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.0 years ago marcin.bazyliszek • 0
0
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1
reply
599
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
1
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1
reply
932
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
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4
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896
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Fix regions for bumphunter
bumphunter DMR methylation minfi
4.2 years ago i.s.brorson • 0
1
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3
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1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.2 years ago erwin.tomasich ▴ 10
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1
reply
807
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Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.2 years ago by ▴ 90 • written 4.3 years ago by • 0
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0
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684
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Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.3 years ago A ▴ 40
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1
reply
2.7k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
4.3 years ago ph.shimaasherif • 0
2
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16
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2.5k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 20
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8
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997
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.3 years ago sara.blocquiaux • 0
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0
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662
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
4.3 years ago luciomora8 • 0
0
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1
reply
956
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
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3
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1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
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3
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1.0k
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trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.5 years ago patriciasolesanchez • 0
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1
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673
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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
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2
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835
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
3
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5
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1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 10
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0
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716
views
DSS for non-CpG site analysis
DSS methylation
4.6 years ago CalM • 0
1
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3
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1.4k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
1
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6
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1.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.6 years ago sabrina.mcnew • 0
1
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4
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1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.8 years ago by ▴ 60 • written 4.8 years ago by • 0
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0
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1.3k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.0 years ago gerald.mccollam • 0
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4
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1.2k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.1 years ago by ★ 6.5k • written 5.1 years ago by • 0
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0
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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 • updated 5.1 years ago moldach ▴ 20
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Answer: Log-cpm values from limma by Gordon Smyth 50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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