Showing : methylation • reset
0
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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 13 months ago by ▴ 20 • written 13 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
13 months ago ramiro.barrantes ▴ 10
1
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3
replies
2.9k
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
889
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
8
replies
1.5k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
0
replies
1.1k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
22 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 23 months ago by ▴ 750 • written 4.5 years ago by • 0
0
votes
7
replies
2.8k
views
error with champ.load
ChAMP champ methylation
updated 2.2 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
replies
935
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
3.3 years ago hlee ▴ 10
2
votes
1
reply
1.1k
views
Limma model orientation
limma methylation MethylationArray
updated 3.5 years ago by 68k • written 3.5 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 3.5 years ago by • 0 • written 10.1 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
votes
0
replies
1.1k
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.7 years ago Lorenzo • 0
0
votes
1
reply
2.4k
views
Gene level methylation values
methylation methylKit bsseq
updated 4.0 years ago by ▴ 10 • written 4.3 years ago by ▴ 80
2
votes
2
replies
1.3k
views
How to overcome issue linked to loading big R object
minfi R methylation
4.5 years ago Federica ▴ 10
1
vote
5
replies
5.5k
views
minfi - error when reading idat files
minfi methylation
updated 3.1 years ago by • 0 • written 8.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.8 years ago epibio ▴ 10
0
votes
1
reply
1.3k
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
5.3 years ago i.s.castanho • 0
0
votes
1
reply
993
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
5.5 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
954
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.6 years ago i.s.castanho • 0
1
vote
1
reply
1.4k
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 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 5.8 years ago by ▴ 90 • written 5.8 years ago by • 0
0
votes
0
replies
1.1k
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.8 years ago A ▴ 60
0
votes
1
reply
3.6k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
5.8 years ago ph.shimaasherif • 0
2
votes
16
replies
4.2k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 5.8 years ago by ▴ 290 • written 5.8 years ago by ▴ 20
0
votes
8
replies
1.6k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.8 years ago sara.blocquiaux • 0
0
votes
0
replies
1.0k
views
Methylmix results are a bit different from beta values results
cancer methylmix methylation betavalues DMvalues
5.8 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 5.9 years ago by ★ 4.0k • written 5.9 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
1.7k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
6.0 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
6.0 years ago sorjuelal • 0
0
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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 6.1 years ago by ▴ 10
0
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0
replies
1.1k
views
DSS for non-CpG site analysis
DSS methylation
6.1 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 2.8 years ago by • 0 • written 6.2 years ago by • 0
1
vote
3
replies
2.1k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by • 0
1
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6
replies
2.9k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.2 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 6.5 years ago by • 0
1
vote
4
replies
2.3k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 6.4 years ago by ▴ 60 • written 6.4 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 6.5 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
6.6 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
1.6k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.7 years ago moldach ▴ 20
142 results • Page 1 of 3
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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