Showing : methylation • reset
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45
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Gene level methylation values
methylation methylKit bsseq
14 days ago ag1805x ▴ 50
1
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1
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104
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Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 11 weeks ago by ▴ 680 • written 11 weeks ago by • 0
2
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2
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134
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How to overcome issue linked to loading big R object
minfi R methylation
12 weeks ago Federica ▴ 10
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2
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1.3k
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minfi - error when reading idat files
minfi methylation
updated 5 months ago by • 0 • written 4.1 years ago by ▴ 10
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0
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236
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
6 months ago Papyrus ▴ 10
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1
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154
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how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 12 months ago by 3.2k • written 12 months ago by ▴ 20
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123
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
12 months ago i.s.castanho • 0
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1
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105
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
14 months ago AishaD • 0
2
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1
reply
161
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
15 months ago Zach Roe ▴ 10
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0
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157
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
15 months ago marcin.bazyliszek • 0
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5
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241
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error with champ.load
ChAMP champ methylation
15 months ago jkong • 0
0
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1
reply
83
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
16 months ago i.s.castanho • 0
1
vote
1
reply
143
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SVA paired samples
SVA EPIC methylation limma
updated 17 months ago by 57k • written 17 months ago by • 0
0
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4
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170
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Fix regions for bumphunter
bumphunter DMR methylation minfi
18 months ago • updated 17 months ago i.s.brorson • 0
1
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3
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232
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
18 months ago erwin.tomasich ▴ 10
1
vote
1
reply
153
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 18 months ago by ▴ 90 • written 18 months ago by • 0
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0
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123
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Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
18 months ago A ▴ 40
0
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1
reply
680
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
18 months ago ph.shimaasherif • 0
2
votes
16
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630
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 18 months ago by ▴ 240 • written 18 months ago by • 0
0
votes
8
replies
219
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DeSeq2: error in design individuals nested within groups
deseq2 methylation
18 months ago sara.blocquiaux • 0
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0
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150
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Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
19 months ago luciomora8 • 0
0
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1
reply
160
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 19 months ago by 3.2k • written 20 months ago by • 0
1
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3
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246
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Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 20 months ago by 57k • written 20 months ago by • 0
1
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3
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226
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
21 months ago patriciasolesanchez • 0
0
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1
reply
172
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Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
21 months ago sorjuelal • 0
0
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2
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231
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 21 months ago by 57k • written 21 months ago by • 0
3
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5
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274
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 21 months ago by 57k • written 22 months ago by ▴ 10
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0
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158
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DSS for non-CpG site analysis
DSS methylation
22 months ago CalM • 0
0
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3
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364
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 23 months ago by ★ 2.6k • written 23 months ago by • 0
1
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3
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300
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
1
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6
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335
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Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
23 months ago sabrina.mcnew • 0
1
vote
2
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936
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3 months ago by • 0 • written 2.2 years ago by • 0
1
vote
4
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453
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 2.1 years ago by ▴ 60 • written 2.1 years ago by • 0
0
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1
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454
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 2.2 years ago by ▴ 240 • written 2.2 years ago by ▴ 20
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0
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393
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.3 years ago gerald.mccollam • 0
4
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4
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405
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.4 years ago by 6.5k • written 2.4 years ago by • 0
0
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0
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421
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
2.5 years ago • updated 2.4 years ago moldach ▴ 20
0
votes
1
reply
315
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
1
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2
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541
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.6 years ago by ★ 1.2k • written 2.6 years ago by • 0
2
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1
reply
497
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 2.7 years ago by ▴ 240 • written 2.7 years ago by • 0
0
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0
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279
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
2.7 years ago saripalligautam86 ▴ 10
0
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2
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756
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
2.8 years ago yuabrahamliu • 0
1
vote
2
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801
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 2.9 years ago by 57k • written 2.9 years ago by ▴ 20
2
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8
replies
655
views
edgeR: design matrix for methylation analysis
edger methylation
updated 2.9 years ago by 43k • written 3.1 years ago by • 0
0
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0
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390
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
2.9 years ago mtkk94 • 0
5
votes
9
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637
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 2.9 years ago by ★ 27k • written 2.9 years ago by • 0
0
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4
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516
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 2.9 years ago by 6.5k • written 2.9 years ago by • 0
1
vote
2
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580
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 2.9 years ago by 25k • written 2.9 years ago by ▴ 10
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3
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574
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
3.0 years ago jbar3141 • 0
1
vote
1
reply
508
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by • 0
50 results • Page 1 of 1
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Comment: Selecting pairs of exons from differentially spliced genes by jamie.gearing ▴ 40
That is fair enough. Sensible is always reassuring to hear! Thanks very much for your input Gordon. Best regards, Jamie.
Answer: Selecting pairs of exons from differentially spliced genes by Gordon Smyth 43k
Choosing a representative pair of exons is not part of our method, so we won't make any recommendations. You should choose the exons wit…
Comment: combineTwoExpressionSet from a4Base is not working properly by russ.bainer • 0
I ran across this bug as well- the issue is related to the code failing to reorder the ExpressionSet rows prior to merging. A workaround fo…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
k has to be odd - trying 9, 21 instead
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…
Votes
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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