[BioC] Beta score of DNA methylation assays

Sonia Shah S.Shah at cs.ucl.ac.uk
Mon Jun 1 15:58:03 CEST 2009

Hi Adai,

I think the beta score is the ratio of intensities between methylated and
unmethylated alleles:

Beta = methylated signal/(unmethylated signal + methylated signal + 100)

So in your case Beta= Cy5/(Cy3+Cy5+100).

A Beta of 0 means the site is completely unmethylated and a value of 1 means
fully methylated.



Adaikalavan Ramasamy wrote:
> Hi there,
> I been handed a tabular file from DNA methylation containing "Beta" 
> values (rows are CpG island and columns are subjects) from Illumina 
> platform. The Beta values range between 0 and 1.
> I am wondering how this "Beta" value is derived, what it means and how 
> to use it.
> Or do I calculate the Cy3/Cy5 ratio and proceed as with gene 
> expression microarray studies?
> Please accept my apologies if these are basic questions and kindly 
> point me to any reference. It is my first DNA methylation dataset. 
> Thank you.
> Regards, Adai
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