Showing : methylationEPIC • reset
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Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
3.9 years ago rmf ▴ 20
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518
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Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
3.9 years ago rmf ▴ 20
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could not find function "champ.load"
ChAMP champ 2.9.10 methylationepic
4.9 years ago • updated 4.8 years ago david.ch • 0
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differential methylation analysis with RnBeads
rnbeads methylation methylationepic dna methylation
4.9 years ago gabrielrfries • 0
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ChAMP Methylation analysis error code "could not find function champ.load"
champ methylationepic
updated 5.0 years ago by ▴ 250 • written 5.0 years ago by • 0
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Error while using champ.svd() function in subset of data
ChAMP methylationepic epicarray epigenomics
updated 5.3 years ago by ▴ 140 • written 5.4 years ago by ▴ 10
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Error when changing the database for minfi dropLociWithSnps
minfi methylationepic illuminahumanmethylationepicanno.ilmn10b.hg19 SNP
5.6 years ago Ellen O • 0
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Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 5.7 years ago by ★ 3.5k • written 5.7 years ago by • 0
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minfi "mapToGenome" dimension error
methylation epic microarray minfi methylationepic
5.9 years ago nhejazi • 0
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Shinymethyl 850K Array quality control signal cutoffs
shinymethyl minfi epic microarray methylationepic qualitycontrol
6.0 years ago chelsey.ju • 0
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MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
6.1 years ago annabelle.congras ▴ 10
11 results • Page 1 of 1
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Answer: msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spect by thomas.nigel.lawson • 0
This has been resolved (Windows Firewall issue) - see github issue https://github.com/computational-metabolomics/msPurity/issues/100
Answer: DESeq2 parameter infernce by Michael Love 39k
We use IRLS which is related to Newton-Raphson method. I suppose you can use any optimization method you prefer. We also sometimes use L-BF…
Answer: DESeq2 with 2 continuous factors, LRT, coeficients and slope by Michael Love 39k
See `?results` which describes what the LFC is when you perform an LRT: "*For analyses using the likelihood ratio test*..." Also in the …
Answer: DESeq2 with sample effect, unequal sample sizes by Michael Love 39k
For statistical analysis plans such as design and coefficient interpretation, I recommend collaborating with a local statistician or someon…
Comment: Bioconductor tool for curating annotations? by Lluís Revilla Sancho ▴ 700
I think you can find those transcripts not overlapping with a GRanges object easily via ?GenomicRanges::setdiff, but I don't know how to an…
Votes
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
A: Limma-voom with external observation weights
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