Hi Tim, Yes your right I need to fit binary model one for present and the other for absent. I have a dataset of 11 disease state arrays and 6 control arrays.This is an affymetrix HG-U133 plus 2 which has 54675 probes.So from this I should get the present probes with the average intensity across all the samples which are above the threshold of where these 2 Gaussian PDF's. I am not a biostatistician, so could you give me the rough code or place where I can easily correlate with my data and fit accordingly to my data. Thanks, Viritha On Wed, Apr 13, 2011 at 4:31 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > what he said. now it's a Bayesian mixture model. ;-) > > > On Wed, Apr 13, 2011 at 1:28 PM, Matthew McCall <mccallm@gmail.com> wrote: > >> Viritha, >> >> For present/absent calls on Affy arrays, you might want to look into >> the barcode function in the frma package. This does something similar >> to what you want to do but uses a huge database of arrays to estimate >> the mixture distribution ahead of time. >> >> Best, >> Matt >> >> On Wed, Apr 13, 2011 at 3:50 PM, viritha kaza <viritha.k@gmail.com> >> wrote: >> > Hi Group, >> > I have GCRMA normalised Affymetrix dataset.With this I wanted to find >> > present and absent probes using Gaussian mixture model,by creating 2 >> > Gaussian probability density function,one for present and the other for >> > absent.The probes whose average intensity across all the samples, larger >> > than threshold value where the 2 gaussian PDFs meet is to be considered >> as >> > present. >> > To do the analysis I was suggested to use Mclust package. But could >> anyone >> > suggest some fuctions in the package that would be useful in this task >> on >> > which I could focus on. >> > Thanks, >> > Viritha >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > >> >> >> >> -- >> Matthew N McCall, PhD >> 112 Arvine Heights >> Rochester, NY 14611 >> Cell: 202-222-5880 >> >> _______________________________________________ >> 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]]