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methylationepic
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Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
6.9 years ago
firestar
▴ 20
0
votes
0
replies
1.2k
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
6.9 years ago
firestar
▴ 20
3
votes
6
replies
2.8k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
7.9 years ago • updated 7.8 years ago
david.ch
• 0
0
votes
0
replies
1.5k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
7.9 years ago
gabrielrfries
• 0
0
votes
1
reply
2.5k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
methylationepic
updated 8.0 years ago by
Yuan Tian
▴ 290 • written 8.0 years ago by
csappleby-mallinder1
• 0
3
votes
4
replies
4.1k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 8.3 years ago by
rcavalca
▴ 140 • written 8.3 years ago by
karthikrpad
▴ 10
0
votes
0
replies
1.3k
views
Error when changing the database for minfi dropLociWithSnps
minfi
methylationepic
illuminahumanmethylationepicanno.ilmn10b.hg19
SNP
8.6 years ago
Ellen O
• 0
0
votes
2
replies
3.1k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 8.7 years ago by
Guido Hooiveld
★ 4.1k • written 8.7 years ago by
Ellen O
• 0
0
votes
4
replies
2.3k
views
minfi "mapToGenome" dimension error
methylation
epic microarray
minfi
methylationepic
8.9 years ago
nhejazi
• 0
0
votes
0
replies
1.5k
views
Shinymethyl 850K Array quality control signal cutoffs
shinymethyl
minfi
epic microarray
methylationepic
qualitycontrol
8.9 years ago
chelsey.ju
• 0
0
votes
3
replies
2.3k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
9.1 years ago
annabelle.congras
▴ 10
11 results • Page
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Answer: Array weights in dpcDE
by
Gordon Smyth
53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…
Answer: lfc shrinkage estimator in DESeq2
by
Michael Love
43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice
by
Gordon Smyth
53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice
by
SamGG
▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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