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

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, Saroj 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >