[BioC] Beta score of DNA methylation assays

Saroj K Mohapatra saroj at vt.edu
Sun May 31 15:50:07 CEST 2009

Hi Adai:

I have not worked with this kind of data myself. But I saw this 
methodology paper (1) that deals with Model-based clustering of DNA 
methylation array data from Illumina GoldenGate methylation platform. 
They have used some R packages in their analysis.

Best wishes,


1. Houseman et al (2008) Model-based clustering of DNA methylation array 
data: a recursive-partitioning algorithm for high-dimensional data 
arising as a mixture of beta distributions. /**BMC Bioinformatics/, 9:365

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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