Hello everybody, I'm very new of R and Infinium methylation analyses. I'm trying to analyze beta-values from an experiment performed by a collegue on Infinium 450k platform. When I plot the distribution of the beta-values, I achieve a distribution with 3 peaks: 1 around 100% methylated (expected), and 2 around respectively 0 and 10% methylation, like in the figure attached. I expected only a peak in this region, i.e. a bimodal distribution. Do you think this could be a normalization or techinical bias? Has anyone ever observed something similar? Thank you in advance, MGiulia

Hi Maria, You will need to post a link to a webpage or some such, the list software strips out attachments. Also your sessionInfo() and any preceding data manipulations that might have been involved would be very helpful. If it's what I think it is, then yes, I've seen it before. --t On Wed, Jun 22, 2011 at 8:05 AM, maria giulia bacalini <mugiu17@hotmail.com>wrote: > > Hello everybody, > > I'm very new of R and Infinium methylation analyses. > I'm trying to analyze beta-values from an experiment performed by a > collegue on Infinium 450k platform. > When I plot the distribution of the beta-values, I achieve a distribution > with 3 peaks: 1 around 100% methylated (expected), and 2 around respectively > 0 and 10% methylation, like in the figure attached. I expected only a peak > in this region, i.e. a bimodal distribution. Do you think this could be a > normalization or techinical bias? Has anyone ever observed something > similar? > > Thank you in advance, > MGiulia > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]