Showing : methylation • reset
2
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2
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50
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How to overcome issue linked to loading big R object
minfi R methylation
3 days ago Federica ▴ 10
0
votes
2
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1.2k
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minfi - error when reading idat files
minfi methylation
updated 11 weeks ago by • 0 • written 3.8 years ago by ▴ 10
0
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0
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177
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3 months ago Papyrus ▴ 10
0
votes
1
reply
104
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 9 months ago by 2.8k • written 9 months ago by ▴ 20
0
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0
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90
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
9 months ago i.s.castanho • 0
0
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1
reply
68
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
11 months ago AishaD • 0
2
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1
reply
121
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lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
12 months ago Zach Roe ▴ 10
0
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0
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107
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
12 months ago marcin.bazyliszek • 0
0
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5
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147
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error with champ.load
ChAMP champ methylation
13 months ago jkong • 0
0
votes
1
reply
52
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
13 months ago i.s.castanho • 0
1
vote
1
reply
101
views
SVA paired samples
SVA EPIC methylation limma
updated 14 months ago by 56k • written 14 months ago by • 0
0
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4
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117
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Fix regions for bumphunter
bumphunter DMR methylation minfi
15 months ago • updated 14 months ago i.s.brorson • 0
1
vote
3
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157
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
15 months ago erwin.tomasich ▴ 10
1
vote
1
reply
103
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 15 months ago by ▴ 90 • written 15 months ago by • 0
0
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0
replies
90
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
15 months ago A ▴ 40
0
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1
reply
513
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
16 months ago ph.shimaasherif • 0
2
votes
16
replies
457
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 16 months ago by ▴ 220 • written 16 months ago by • 0
0
votes
8
replies
154
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
16 months ago sara.blocquiaux • 0
0
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0
replies
109
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
16 months ago luciomora8 • 0
0
votes
1
reply
122
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 17 months ago by 2.8k • written 17 months ago by • 0
1
vote
3
replies
196
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 17 months ago by 56k • written 17 months ago by • 0
1
vote
3
replies
163
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
18 months ago patriciasolesanchez • 0
0
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1
reply
127
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
18 months ago sorjuelal • 0
0
votes
2
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186
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 19 months ago by 56k • written 19 months ago by • 0
2
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5
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216
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DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 19 months ago by 56k • written 19 months ago by • 0
0
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0
replies
120
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DSS for non-CpG site analysis
DSS methylation
19 months ago CalM • 0
0
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3
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277
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WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 20 months ago by ★ 2.6k • written 20 months ago by • 0
1
vote
3
replies
233
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 20 months ago by ▴ 10 • written 20 months ago by • 0
1
vote
6
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249
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
20 months ago sabrina.mcnew • 0
1
vote
2
replies
703
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 15 days ago by • 0 • written 2.0 years ago by • 0
1
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4
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380
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 22 months ago by ▴ 60 • written 22 months ago by • 0
0
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1
reply
403
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 2.0 years ago by ▴ 220 • written 2.0 years ago by ▴ 20
0
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0
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343
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.1 years ago gerald.mccollam • 0
4
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4
replies
346
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.2 years ago by 6.5k • written 2.2 years ago by • 0
0
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0
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376
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
2.2 years ago moldach ▴ 20
0
votes
1
reply
284
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 2.3 years ago by 56k • written 2.3 years ago by • 0
1
vote
2
replies
480
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.4 years ago by ★ 1.2k • written 2.4 years ago by • 0
2
votes
1
reply
427
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 2.4 years ago by ▴ 220 • written 2.5 years ago by • 0
0
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0
replies
245
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
2.5 years ago saripalligautam86 ▴ 10
0
votes
2
replies
650
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
2.6 years ago yuabrahamliu • 0
1
vote
2
replies
707
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 2.6 years ago by 56k • written 2.6 years ago by ▴ 20
2
votes
8
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583
views
edgeR: design matrix for methylation analysis
edger methylation
updated 2.6 years ago by 42k • written 2.8 years ago by • 0
0
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0
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343
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
2.6 years ago mtkk94 • 0
5
votes
9
replies
558
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 2.7 years ago by ★ 26k • written 2.7 years ago by • 0
0
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4
replies
438
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 2.7 years ago by 6.5k • written 2.7 years ago by • 0
1
vote
2
replies
505
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 2.7 years ago by 25k • written 2.7 years ago by ▴ 10
0
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3
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488
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
2.7 years ago jbar3141 • 0
1
vote
1
reply
437
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 2.8 years ago by ▴ 20 • written 2.8 years ago by • 0
0
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0
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409
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
2.8 years ago sichan • 0
0
votes
2
replies
390
views
MethylKit DSS Package
R bioconductor methylation methylkit
updated 2.8 years ago by ▴ 20 • written 2.8 years ago by • 0
129 results • Page 1 of 3
Recent ...
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Comment: Compute fgsea with my own database with R version 4.0.2 by assaron ▴ 190
I'm not sure what would be the best course of action in your case, if there is one at all, but I'd suggest to keep the ranking on the gene-…
Comment: Error installing Deseq2 by ATpoint ▴ 590
Go through the error logs and find the first error, this is where you have to start debugging, this here is just the consequences of the in…
Answer: "No genes can be mapped...." using enrichGO in clusterProfiler by Guido Hooiveld ★ 2.9k
It must be something at your end, because for me it is working. I think it is either due to a wrong input, or because your are 'looping'. …
Comment: Is there a different way to generate a tree for phyloseq object by Axel Klenk ▴ 980
1058 sounds much, much better. :-) Good to hear you got it done. Cheers, - axel
Comment: studying periodicity among small number of gene transcripts by matthew.carlucci • 0
Yes, DiscoRhythm can be used for matrices of all sizes, as long as each gene/row has enough collected data. The main `discoODAs()` ("Oscill…
Votes
Comment: DESeq2 with high range of within-group variability
Comment: problem regarding differential gene express analysis
Comment: Normalisation in DESeq2
Answer: Compute fgsea with my own database with R version 4.0.2
Comment: lmFit, number of proteins
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