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dmrseq
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0
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374
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dmrseq on a subset of genomic regions
dmrseq
updated 22 months ago by
keegan
▴ 60 • written 23 months ago by
KIR_F
• 0
0
votes
0
replies
473
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
2.8 years ago
marcin.bazyliszek
• 0
0
votes
1
reply
370
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
3.3 years ago
sorjuelal
• 0
0
votes
1
reply
464
views
unequal sample sizes in groups for testCovariate argument in dmrseq
dmrseq
3.5 years ago
Stephanie Hicks
▴ 80
0
votes
1
reply
741
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq
sva
DSS
updated 3.6 years ago by
keegan
▴ 60 • written 3.6 years ago by
gjl
• 0
1
vote
4
replies
840
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 3.6 years ago by
keegan
▴ 60 • written 3.6 years ago by
sorjuelal
• 0
6
votes
5
replies
835
views
dmrseq installation failed
installation problem
dmrseq
bumphunter
updated 4.2 years ago by
shepherl
3.4k • written 4.2 years ago by
guy.bioinfo
▴ 10
3
votes
16
replies
1.2k
views
Internal bug of DMR-Seq?
dmrseq
updated 4.3 years ago by
keegan
▴ 60 • written 4.3 years ago by
kuckunniwid
• 0
0
votes
3
replies
595
views
DMRseq smoothed values
dmrseq
updated 4.5 years ago by
keegan
▴ 60 • written 4.5 years ago by
swebb1
• 0
0
votes
3
replies
700
views
Determination of Hypo- or Hyper- methylation
dmrseq
bsseq
updated 4.7 years ago by
James W. MacDonald
62k • written 4.7 years ago by
Bruno Verstraeten
• 0
2
votes
2
replies
975
views
dmrseq: cannot adjust for a covariate
dmrseq
dmr
dmrs
bisulfite
methylation
updated 5.0 years ago by
keegan
▴ 60 • written 5.0 years ago by
l.kremer
• 0
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Michael Love
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The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
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That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
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You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
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Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
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