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rrbs
•
reset
4
votes
5
replies
1.0k
views
edgeR for a mixture experiment
edgeR
model-selection
RRBS
mixture-experiment
3.1 years ago
ingerslev
• 0
0
votes
2
replies
837
views
MethylCC for RRBS data of Cord Blood
MethylCC
RRBS
cord blood
3.8 years ago
weichen-cls
• 0
0
votes
0
replies
750
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
3.8 years ago
i.s.castanho
• 0
0
votes
1
reply
608
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.1 years ago
i.s.castanho
• 0
5
votes
14
replies
2.0k
views
Odd P-value distribution in edgeR on RRBS data
edgeR
rrbs
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
ingerslev
• 0
0
votes
4
replies
2.2k
views
MethylKit read in issue
methykit
rrbs
updated 6.0 years ago by
Mike Smith
★ 6.5k • written 6.0 years ago by
bekah
▴ 40
0
votes
3
replies
1.5k
views
scalability of edgeR on RRBS methylation data
edgeR
methyation
RRBS
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
osa.zuta
▴ 40
0
votes
1
reply
1.1k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.1 years ago
l.eijssen
• 0
1
vote
4
replies
1.8k
views
Using SVA with RRBS data
sva
RRBS
updated 7.1 years ago by
Jeff Leek
▴ 650 • written 7.1 years ago by
mrodrigues.fernanda
▴ 10
0
votes
3
replies
1.7k
views
SVA package for RRBS - bisulfite methylation data
rrbs
batch effect
methylation
sva
updated 7.6 years ago by
dashbrook1
• 0 • written 8.8 years ago by
GFM
▴ 20
4
votes
2
replies
1.4k
views
Bounded Regression with Limma for RRBS?
limma
rrbs
bsseq
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
nhejazi
• 0
0
votes
5
replies
2.0k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.0 years ago
maria.maqueda
• 0
12 results • Page
1 of 1
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Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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tangming2005
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