Hi all, I have 1. an affy object that contains all my normalized data, the result from rma. 2. an affy object that contains P/M/A calls, the result from mas5calls. I now want to eliminate probe sets from my normalized data that are absent in all my samples. I then want to set up a contrast matrix and fit a model using probesets that are only present in ALL samples. Does anyone know how I can extract this subset of data from my object in 1? Thanks! [[alternative HTML version deleted]]

Hi Supriya, On 5/19/2011 3:39 PM, Supriya Munshaw wrote: > Hi all, > > I have > > 1. an affy object that contains all my normalized data, the > result from rma. > > 2. an affy object that contains P/M/A calls, the result from > mas5calls. > > I now want to eliminate probe sets from my normalized data that are > absent in all my samples. I then want to set up a contrast matrix and > fit a model using probesets that are only present in ALL samples. > > Does anyone know how I can extract this subset of data from my object > in 1? Let's say your ExpressionSet containing the mas5calls is called 'mcalls', and the ExpressionSet containing the rma data is called 'eset'. ind <- apply(exprs(mcalls), 1, function(x) all(x == "A")) filteredEset <- eset[!ind,] Best, Jim > > Thanks! > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues