Hi. I am trying to use expressopdnn function to generate expression measure. The commands that I use are listed below, the calculations take a very long time (therefore takes ages to trouble shoot) but only return NA values. If I substitute exampleData, with my data it doesn't work at all. Can someone please help. library(affy) library(affypdnn) library(hgu133aprobe) library(matchprobes) data<-ReadAffy() energy.file<-system.file("exampleData","pdnn-energy-parameter_hg- u133a.txt",package="affypdnn") params.chiptype<-pdnn.params.chiptype(energy.file,probes.pack="hgu133a probe") data.pdnn<-expressopdnn(data,bg.correct=FALSE,normalize.method="quanti les",params.chiptype=params.chiptype) data.pdnnpredict<-expressopdnn(data,bg.correct=FALSE,normalize.method= "quantiles",pmcorrect.method="pdnnpredict",params.chiptype=params.chip type) -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au