Bioconductor DmpFinder

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methylset minfi dmpFinder betaHMM beta

updated 7 months ago by James W. MacDonald 68k • written 7 months ago by neyousha • 0

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minfi limma lmm lmfit dmpFinder

4.0 years ago kyleyxw • 0

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minfi methylation dmpfinder limma

updated 8.0 years ago by vulegom • 0 • written 8.7 years ago by mcall ▴ 20

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minfi dmpfinder dmp illuminahumanmethylationepicanno.ilmn10b.hg19 epic microarray

updated 8.9 years ago by James W. MacDonald 68k • written 8.9 years ago by Biologist ▴ 120

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2.3k

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minfi minfidata illumina methylation dmpfinder

updated 10.7 years ago by James W. MacDonald 68k • written 10.7 years ago by michael.zulyniak • 0

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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0

Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…

Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0

The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …

Comment: parameters of filterByExpr by Paul Harrison ▴ 110

It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

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Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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