On Mon, Jun 1, 2009 at 12:04 PM, Adaikalavan Ramasamy <a.ramasamy at="" imperial.ac.uk=""> wrote: > 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. Hi, Adai. Thanks for the comments. The goal of the package is really to parse the data and apply a reasonable normalization to the data. There are certainly robust tests that could be used for statistical purposes. That said, the distribution of Beta values within a sample across CpG sites (which always has the bimodality you mention) is not the distribution of interest, I'm sure you know better than I (I'm no statistician!). Instead, you want to examine the distribution of beta values for a given CpG site within the two populations of interest. I have not looked at this in any detail, but if those two distributions approach normality, then a t-test may be appropriate. So, in short, there is a bit of a gray area here. I should probably add some disclaimer to the vignette to that effect. Sean > > 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 >>> >> >> >> > > _______________________________________________ > 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 >