Question: DNA methylation analysis with RnBeads: start analysis from Beta-values
0
gravatar for nick
20 months ago by
nick70
nick70 wrote:

I am trying to use RnBeads to analyze DNA-methylation data, but I already have a matrix of beta-values. I cannot find a way to import data in that format and launch a differential analysis. Has anyone encountered the same problem?

rnbeads dna-methylation • 960 views
ADD COMMENTlink modified 20 months ago by andrew.j.skelton734.2k • written 20 months ago by nick70

What kind of analysis do you want to perform? Differential Methylation?

ADD REPLYlink written 20 months ago by andrew.j.skelton734.2k

Yes, sorry I didn't specify that.

ADD REPLYlink written 20 months ago by nick70
1
gravatar for andrew.j.skelton73
20 months ago by
Newcastle Upon Tyne
andrew.j.skelton734.2k wrote:

If you have normalised Beta values, and you trust the normalisation method (i.e. there's no way to get the IDAT files), then you can simply read that into R, convert to M values:

m <- log2(beta/(1 - beta))

Then perform a differential methylation analysis using Limma

ADD COMMENTlink modified 20 months ago • written 20 months ago by andrew.j.skelton734.2k
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