Dear All, I'm looking at some older affy data from the Hu6800 arrays. In the Affy package I'm normalising by either mas5 or by RMA which is working fine. However when I try to generate P/M/A calls by: "Calls<-mas5calls(Data)" I get the following output and error message: Getting probe level data... Computing p-values Making P/M/A Calls Error in if (y < alpha1) { : missing value where TRUE/FALSE needed I have done the same type of treatment on U95 arrays and it works perfectly. Any ideas as to why the Hu6800 chips are causing a problem? And more importantly, any idea of how to get it working or of an alternative way to generate P/M/A calls? Most of the data I want to look at is of this format so any help would be very gratefully received. Thanks, Euan p.s. I am very much of the "newbie" category wrt R so if you can keep it simple that would be great! (R 2.0.0 on windows xp with default Bioconductor packages installed) -- Euan Stronach, PhD Research Associate Section of Molecular Therapeutics Department of Cancer Medicine Imperial College London 7th Floor Laboratories MRC Cyclotron Building Du Cane Road London W12 ONN E-mail: e.stronach@imperial.ac.uk Mobile: +44 (0)7762 900661 Office/Lab: +44 (0)208 3838 345 Fax: +44 (0)208 3838 349

Dear All, I'm looking at some older affy data from the Hu6800 arrays. In the Affy package I'm normalising by either mas5 or by RMA which is working fine. However when I try to generate P/M/A calls by: "Calls<-mas5calls(Data)" I get the following output and error message: Getting probe level data... Computing p-values Making P/M/A Calls Error in if (y < alpha1) { : missing value where TRUE/FALSE needed I have done the same type of treatment on U95 arrays and it works perfectly. Any ideas as to why the Hu6800 chips are causing a problem? And more importantly, any idea of how to get it working or of an alternative way to generate P/M/A calls? Most of the data I want to look at is of this format so any help would be very gratefully received. Thanks, Euan p.s. I am very much of the "newbie" category wrt R so if you can keep it simple that would be great! (R 2.0.0 on windows xp with default Bioconductor packages installed) -- Euan Stronach, PhD Research Associate Section of Molecular Therapeutics Department of Cancer Medicine Imperial College London 7th Floor Laboratories MRC Cyclotron Building Du Cane Road London W12 ONN E-mail: e.stronach@imperial.ac.uk Mobile: +44 (0)7762 900661 Office/Lab: +44 (0)208 3838 345 Fax: +44 (0)208 3838 349 [[alternative HTML version deleted]]