Showing : methylation • reset
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149
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
6 months ago hlee • 0
2
votes
1
reply
234
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Limma model orientation
limma methylation MethylationArray
updated 8 months ago by 62k • written 8 months ago by • 0
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2
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1.9k
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Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 9 months ago by • 0 • written 7.3 years ago by ▴ 10
1
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1
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309
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 10 months ago by ▴ 80 • written 10 months ago by ▴ 10
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0
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272
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WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
11 months ago Lorenzo • 0
0
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1
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430
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Gene level methylation values
methylation methylKit bsseq
updated 15 months ago by ▴ 10 • written 18 months ago by ▴ 50
1
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1
reply
534
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Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 21 months ago by ▴ 730 • written 21 months ago by • 0
2
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2
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456
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How to overcome issue linked to loading big R object
minfi R methylation
21 months ago Federica ▴ 10
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5
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2.5k
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minfi - error when reading idat files
minfi methylation
updated 4 months ago by • 0 • written 5.6 years ago by ▴ 10
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0
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565
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
2.0 years ago epibio ▴ 10
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1
reply
453
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how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 2.5 years ago by 3.7k • written 2.5 years ago by ▴ 20
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0
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348
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
2.5 years ago i.s.castanho • 0
0
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1
reply
309
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
2.7 years ago AishaD • 0
2
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1
reply
505
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
2.8 years ago Zach Roe ▴ 10
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0
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462
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
2.8 years ago marcin.bazyliszek • 0
0
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6
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805
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error with champ.load
ChAMP champ methylation
updated 18 months ago by • 0 • written 2.8 years ago by • 0
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1
reply
288
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
2.8 years ago i.s.castanho • 0
1
vote
1
reply
495
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SVA paired samples
SVA EPIC methylation limma
updated 2.9 years ago by 62k • written 2.9 years ago by • 0
0
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4
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448
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
3.0 years ago i.s.brorson • 0
1
vote
3
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769
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Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
3.0 years ago erwin.tomasich ▴ 10
1
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1
reply
472
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Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 3.0 years ago by ▴ 90 • written 3.0 years ago by • 0
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0
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329
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Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
3.0 years ago A ▴ 40
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1
reply
1.8k
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r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
3.1 years ago ph.shimaasherif • 0
2
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16
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1.3k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 3.1 years ago by ▴ 250 • written 3.1 years ago by ▴ 10
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8
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504
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DeSeq2: error in design individuals nested within groups
deseq2 methylation
3.1 years ago sara.blocquiaux • 0
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0
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367
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
3.1 years ago luciomora8 • 0
0
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1
reply
522
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 3.1 years ago by 3.7k • written 3.1 years ago by • 0
1
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3
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593
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Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 3.2 years ago by 62k • written 3.2 years ago by • 0
1
vote
3
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546
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
3.2 years ago patriciasolesanchez • 0
0
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1
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368
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Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
3.3 years ago sorjuelal • 0
0
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2
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510
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 3.3 years ago by 62k • written 3.3 years ago by • 0
3
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5
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691
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DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 3.3 years ago by 62k • written 3.3 years ago by ▴ 10
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0
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356
views
DSS for non-CpG site analysis
DSS methylation
3.4 years ago CalM • 0
0
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4
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830
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WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 10 days ago by • 0 • written 3.4 years ago by • 0
1
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3
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860
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 3.4 years ago by ▴ 10 • written 3.4 years ago by • 0
1
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6
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786
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Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
3.4 years ago sabrina.mcnew • 0
1
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2
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2.2k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 21 months ago by • 0 • written 3.7 years ago by • 0
1
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4
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825
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dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 3.6 years ago by ▴ 60 • written 3.6 years ago by • 0
0
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1
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1.1k
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 3.7 years ago by ▴ 250 • written 3.7 years ago by ▴ 20
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824
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
3.8 years ago gerald.mccollam • 0
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4
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728
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Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 3.9 years ago by 6.5k • written 3.9 years ago by • 0
0
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0
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722
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
4.0 years ago • updated 3.9 years ago moldach ▴ 20
0
votes
1
reply
545
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 4.0 years ago by 62k • written 4.0 years ago by • 0
1
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2
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937
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 4.1 years ago by ★ 1.3k • written 4.1 years ago by • 0
2
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1
reply
807
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 4.2 years ago by ▴ 250 • written 4.2 years ago by • 0
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0
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480
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
4.2 years ago saripalligautam86 ▴ 10
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2
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1.5k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
4.3 years ago yuabrahamliu • 0
1
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2
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1.4k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 4.4 years ago by 62k • written 4.4 years ago by ▴ 20
2
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8
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1.1k
views
edgeR: design matrix for methylation analysis
edger methylation
updated 4.4 years ago by 47k • written 4.6 years ago by • 0
0
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0
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589
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Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
4.4 years ago mtkk94 • 0
50 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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