Showing : methylation • reset
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198
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Gene level methylation values
methylation methylKit bsseq
updated 3 months ago by ▴ 10 • written 6 months ago by ▴ 50
1
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1
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268
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Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 8 months ago by ▴ 710 • written 8 months ago by • 0
2
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2
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252
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How to overcome issue linked to loading big R object
minfi R methylation
9 months ago Federica ▴ 10
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2
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1.6k
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minfi - error when reading idat files
minfi methylation
updated 11 months ago by • 0 • written 4.6 years ago by ▴ 10
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0
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349
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
12 months ago epibio ▴ 10
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1
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244
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how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 18 months ago by 3.4k • written 18 months ago by ▴ 20
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197
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
18 months ago i.s.castanho • 0
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1
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176
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
20 months ago AishaD • 0
2
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1
reply
263
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
21 months ago Zach Roe ▴ 10
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0
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268
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
21 months ago marcin.bazyliszek • 0
0
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6
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467
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error with champ.load
ChAMP champ methylation
updated 5 months ago by • 0 • written 21 months ago by • 0
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1
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146
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
22 months ago i.s.castanho • 0
1
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1
reply
250
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SVA paired samples
SVA EPIC methylation limma
updated 23 months ago by 58k • written 23 months ago by • 0
0
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4
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275
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Fix regions for bumphunter
bumphunter DMR methylation minfi
24 months ago • updated 23 months ago i.s.brorson • 0
1
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3
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399
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Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
2.0 years ago erwin.tomasich ▴ 10
1
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1
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255
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Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 2.0 years ago by ▴ 90 • written 2.0 years ago by • 0
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0
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195
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
2.0 years ago A ▴ 40
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1
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1.1k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
2.1 years ago ph.shimaasherif • 0
2
votes
16
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936
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 2.1 years ago by ▴ 240 • written 2.1 years ago by • 0
0
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8
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313
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DeSeq2: error in design individuals nested within groups
deseq2 methylation
2.1 years ago sara.blocquiaux • 0
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0
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224
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Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
2.1 years ago luciomora8 • 0
0
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1
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280
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Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 2.1 years ago by 3.4k • written 2.1 years ago by • 0
1
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3
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408
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Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
1
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3
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329
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trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
2.2 years ago patriciasolesanchez • 0
0
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1
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240
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Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
2.3 years ago sorjuelal • 0
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2
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314
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 2.3 years ago by 58k • written 2.3 years ago by • 0
3
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5
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412
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 2.3 years ago by 58k • written 2.3 years ago by ▴ 10
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0
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228
views
DSS for non-CpG site analysis
DSS methylation
2.4 years ago CalM • 0
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3
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538
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WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 2.4 years ago by ★ 2.6k • written 2.4 years ago by • 0
1
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3
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456
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by • 0
1
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6
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440
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Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
2.4 years ago sabrina.mcnew • 0
1
vote
2
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1.4k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 9 months ago by • 0 • written 2.7 years ago by • 0
1
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4
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580
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 2.6 years ago by ▴ 60 • written 2.6 years ago by • 0
0
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1
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657
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 2.7 years ago by ▴ 240 • written 2.7 years ago by ▴ 20
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525
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.8 years ago gerald.mccollam • 0
4
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4
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518
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.9 years ago by 6.5k • written 2.9 years ago by • 0
0
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0
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523
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
3.0 years ago • updated 2.9 years ago moldach ▴ 20
0
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1
reply
379
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 3.0 years ago by 58k • written 3.0 years ago by • 0
1
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2
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737
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 3.1 years ago by ★ 1.3k • written 3.1 years ago by • 0
2
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1
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611
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EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 3.2 years ago by ▴ 240 • written 3.2 years ago by • 0
0
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0
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362
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
3.2 years ago saripalligautam86 ▴ 10
0
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2
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1.1k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
3.3 years ago yuabrahamliu • 0
1
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2
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1.0k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 3.4 years ago by 58k • written 3.4 years ago by ▴ 20
2
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8
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781
views
edgeR: design matrix for methylation analysis
edger methylation
updated 3.4 years ago by 44k • written 3.6 years ago by • 0
0
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0
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460
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
3.4 years ago mtkk94 • 0
5
votes
9
replies
746
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
0
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4
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660
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 3.4 years ago by 6.5k • written 3.4 years ago by • 0
1
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2
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711
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 3.4 years ago by 25k • written 3.4 years ago by ▴ 10
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3
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748
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
3.5 years ago jbar3141 • 0
1
vote
1
reply
685
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 3.5 years ago by ▴ 20 • written 3.5 years ago by • 0
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
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Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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