[BioC] Beta score of DNA methylation assays

[Adaikalavan Ramasamy]

Sonia Shah, thanks for the link. The Beta score is calculated as you 
said with the addition that any negative values of Cy3 and Cy5 are set 
to zero.

Sean Davis, thanks for pointing out to the methylumi package. It looks 
like a nice package. I am slightly concerned that you are analyzing the 
Beta scores without any data transformation (though I like how you 
illustrated it using the limma package). The Beta values appear to be 
highly bimodal and the model near zero seems to be more pronounced. 
Having said that, I also seen others using t-test to analyze the data 
too so I think data tranformation may be a more general problem. Or 
maybe I am worrying too much.

Saroj Mohaptra, thanks for pointing out to Houseman et al. I don't fully 
understand this method yet but will look further into it. Thanks.

Thank you all.

Regards, Adai



Sonia Shah wrote:
> 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.
> 
> See:
> http://www.illumina.com/downloads/DNAMethylationAnalysis_DataSheet.pdf
> 
> 
> 
> Regards,
> Sonia
> 
> 
> 
> 
> 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
>>
> 
> 
>