Showing : Methylation • reset
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218
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 23 days ago by ▴ 170 • written 23 days ago by • 0
0
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1
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145
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 24 days ago by 65k • written 26 days ago by • 0
1
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8
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528
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 3 months ago by • 0
0
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0
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244
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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
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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 5 months ago by • 0 • written 5.0 years ago by ▴ 20
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 4.0 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
replies
3.3k
views
Normalization starting from beta values in minfi
methylation minfi
written 7.9 years ago by ▴ 290
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2
replies
742
views
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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1.6k
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
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
1
vote
0
replies
563
views
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
views
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
reply
649
views
Limma model orientation
limma methylation MethylationArray
updated 24 months ago by 65k • written 24 months ago by • 0
0
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2
replies
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
reply
777
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
0
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0
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723
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
2.2 years ago Lorenzo • 0
0
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1
reply
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
votes
2
replies
860
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
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2
replies
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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960
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
856
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 3.8 years ago by ▴ 20
0
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0
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746
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
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1
reply
637
views
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
978
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
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0
replies
874
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
605
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
1
vote
1
reply
942
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.2 years ago by • 0
0
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4
replies
903
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
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
4.2 years ago erwin.tomasich ▴ 10
1
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1
reply
818
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by • 0
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0
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692
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
4.3 years ago A ▴ 40
0
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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
votes
16
replies
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 ▴ 280 • written 4.3 years ago by ▴ 20
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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
replies
671
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
967
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
vote
3
replies
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
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
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1
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689
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
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2
replies
850
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
726
views
DSS for non-CpG site analysis
DSS methylation
4.6 years ago CalM • 0
1
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3
replies
1.4k
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
replies
1.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.7 years ago sabrina.mcnew • 0
1
vote
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
votes
0
replies
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
replies
1.3k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.1 years ago by ★ 6.5k • written 5.1 years ago by • 0
0
votes
0
replies
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
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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