Showing : methylation • reset
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5
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2.4k
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Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
written 9.2 years ago by • 0
0
votes
13
replies
2.0k
views
When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 12 months ago by ▴ 20 • written 12 months ago by ▴ 10
1
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2
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1.1k
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
12 months ago ramiro.barrantes ▴ 10
1
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3
replies
2.8k
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
updated 12 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
872
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
8
replies
1.5k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
0
replies
1.1k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
21 months ago kyj2226 • 0
1
vote
3
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2.5k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 22 months ago by ▴ 750 • written 4.4 years ago by • 0
0
votes
7
replies
2.7k
views
error with champ.load
ChAMP champ methylation
updated 2.1 years ago by • 0 • written 5.5 years ago by • 0
0
votes
2
replies
1.3k
views
error in champ.SVD
svd methylation champ
updated 2.5 years ago by 4.2k • written 2.5 years ago by • 0
1
vote
0
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927
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
3.2 years ago hlee ▴ 10
2
votes
1
reply
1.0k
views
Limma model orientation
limma methylation MethylationArray
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
votes
2
replies
3.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.4 years ago by • 0 • written 10.0 years ago by ▴ 10
1
vote
1
reply
1.2k
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by ▴ 10
0
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0
replies
1.1k
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.7 years ago Lorenzo • 0
0
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1
reply
2.3k
views
Gene level methylation values
methylation methylKit bsseq
updated 4.0 years ago by ▴ 10 • written 4.2 years ago by ▴ 80
2
votes
2
replies
1.3k
views
How to overcome issue linked to loading big R object
minfi R methylation
4.4 years ago Federica ▴ 10
1
vote
5
replies
5.4k
views
minfi - error when reading idat files
minfi methylation
updated 3.0 years ago by • 0 • written 8.3 years ago by ▴ 10
0
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0
replies
1.4k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.7 years ago epibio ▴ 10
0
votes
1
reply
1.2k
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation epigenomics slurm mpi methylmix
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
5.2 years ago i.s.castanho • 0
0
votes
1
reply
975
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
5.4 years ago AishaD • 0
2
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1
reply
1.4k
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
5.4 years ago Zach Roe ▴ 10
0
votes
0
replies
1.3k
views
Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
5.5 years ago marcin.bazyliszek • 0
0
votes
1
reply
938
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.5 years ago i.s.castanho • 0
1
vote
1
reply
1.3k
views
SVA paired samples
SVA EPIC methylation limma
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
4
replies
1.4k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.7 years ago • updated 5.6 years ago i.s.brorson • 0
1
vote
3
replies
2.0k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.7 years ago erwin.tomasich ▴ 10
1
vote
1
reply
1.2k
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 5.7 years ago by ▴ 90 • written 5.7 years ago by • 0
0
votes
0
replies
1.0k
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.7 years ago A ▴ 60
0
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1
reply
3.5k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
5.7 years ago ph.shimaasherif • 0
2
votes
16
replies
4.1k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.7 years ago by ▴ 290 • written 5.7 years ago by ▴ 20
0
votes
8
replies
1.6k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.7 years ago sara.blocquiaux • 0
0
votes
0
replies
996
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.7 years ago luciomora8 • 0
0
votes
1
reply
1.6k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
1
vote
3
replies
1.6k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
3
replies
1.6k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
5.9 years ago patriciasolesanchez • 0
0
votes
1
reply
1.1k
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq methylation
5.9 years ago sorjuelal • 0
0
votes
2
replies
1.2k
views
Illumina 450K quality controls with meffil
meffil EWAS methylation
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
3
votes
5
replies
2.0k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
0
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0
replies
1.1k
views
DSS for non-CpG site analysis
DSS methylation
6.0 years ago CalM • 0
0
votes
4
replies
2.5k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 2.7 years ago by • 0 • written 6.1 years ago by • 0
1
vote
3
replies
2.1k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
1
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6
replies
2.8k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.1 years ago sabrina.mcnew • 0
1
vote
2
replies
4.8k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 4.5 years ago by • 0 • written 6.4 years ago by • 0
1
vote
4
replies
2.3k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 6.3 years ago by ▴ 60 • written 6.3 years ago by • 0
0
votes
2
replies
2.8k
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 23 months ago by • 0 • written 6.4 years ago by ▴ 20
0
votes
0
replies
1.6k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
6.5 years ago gerald.mccollam • 0
4
votes
4
replies
1.8k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 6.6 years ago by ★ 6.5k • written 6.6 years ago by • 0
0
votes
0
replies
1.5k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.6 years ago moldach ▴ 20
142 results • Page 1 of 3
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Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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