Showing : methylation • reset
1
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322
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
5 weeks ago • updated 6 days ago Kim • 0
0
votes
1
reply
165
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
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8
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552
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
replies
266
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
1
vote
3
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1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
0
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7
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1.8k
views
error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.1 years ago by • 0
0
votes
2
replies
758
views
error in champ.SVD
svd methylation champ
updated 13 months ago by 3.9k • written 13 months ago by • 0
1
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0
replies
578
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
2
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1
reply
658
views
Limma model orientation
limma methylation MethylationArray
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
0
votes
2
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2.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.0 years ago by • 0 • written 8.6 years ago by ▴ 10
1
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1
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784
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.2 years ago by ▴ 90 • written 2.2 years ago by ▴ 10
0
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0
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736
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.3 years ago Lorenzo • 0
0
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1
reply
1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.6 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
2
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2
replies
874
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
1
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5
replies
4.2k
views
minfi - error when reading idat files
minfi methylation
updated 20 months ago by • 0 • written 6.8 years ago by ▴ 10
0
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0
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971
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
0
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1
reply
869
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by ▴ 20
0
votes
0
replies
752
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
3.8 years ago i.s.castanho • 0
0
votes
1
reply
646
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.0 years ago AishaD • 0
2
votes
1
reply
995
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
0
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0
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884
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
4.1 years ago marcin.bazyliszek • 0
0
votes
1
reply
612
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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
vote
1
reply
951
views
SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
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4
replies
919
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
4.3 years ago • updated 4.2 years ago i.s.brorson • 0
1
vote
3
replies
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.3 years ago erwin.tomasich ▴ 10
1
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1
reply
825
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by • 0
0
votes
0
replies
705
views
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
2.8k
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
replies
2.6k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by ▴ 20
0
votes
8
replies
1.0k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
4.3 years ago sara.blocquiaux • 0
0
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0
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677
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
4.3 years ago luciomora8 • 0
0
votes
1
reply
981
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
1
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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 4.5 years ago by 65k • written 4.5 years ago by • 0
1
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3
replies
1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.5 years ago patriciasolesanchez • 0
0
votes
1
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698
views
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
votes
2
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859
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.6 years ago by 65k • written 4.6 years ago by ▴ 10
0
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0
replies
732
views
DSS for non-CpG site analysis
DSS methylation
4.6 years ago CalM • 0
0
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4
replies
1.6k
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 4.7 years ago by • 0
1
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3
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1.5k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.7 years ago by ▴ 10 • written 4.7 years ago by • 0
1
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6
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1.7k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.7 years ago sabrina.mcnew • 0
1
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2
replies
3.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.1 years ago by • 0 • written 5.0 years ago by • 0
1
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4
replies
1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.9 years ago by ▴ 60 • written 4.9 years ago by • 0
0
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2
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2.0k
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 6 months ago by • 0 • written 5.0 years ago by ▴ 20
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
5.1 years ago gerald.mccollam • 0
4
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4
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1.3k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.2 years ago by ★ 6.5k • written 5.2 years ago by • 0
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 moldach ▴ 20
0
votes
1
reply
929
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
1
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2
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1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
2
votes
1
reply
1.3k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 5.5 years ago by ▴ 280 • written 5.5 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Votes
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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