Dear all, We have developed our own Affymetrix chip (Custom Express Array, PM-only with two species). I want to analyse the data with the limma package, but for that I need to built my own CDF package, probe package and built the filters to analyse one specie or another. I'm using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message: Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument I already tried an old version of R-2.9.1 with a package matchprobes (that is no longer update for R-2.13.0) but the same error occurs. Does anyone knows how could I overcome this problem? Thank you very much for your attention. Best Regards, Helga -- Helga Garcia PhD student Applied and Environmental Mycology Lab/Molecular Thermodynamics Lab ITQB I - UNL Portugal [[alternative HTML version deleted]]
Dear all, We have developed our own Affymetrix chip (Custom Express Array, PM-only with two species). I want to analyse the data with the limma package, but for that I need to built my own CDF package, probe package and built the filters to analyse one specie or another. I'm using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message: Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument I already tried an old version of R-2.9.1 with a package matchprobes (that is no longer update for R-2.13.0) but the same error occurs. Does anyone knows how could I overcome this problem? Thank you very much for your attention. Best Regards, Helga -- Helga Garcia PhD student Applied and Environmental Mycology Lab/Molecular Thermodynamics Lab ITQB I - UNL Portugal [[alternative HTML version deleted]]
On 05/08/2011 02:15 PM, Helga Garcia wrote:> Dear all, > > We have developed our own Affymetrix chip (Custom Express Array, PM-only > with two species). > I want to analyse the data with the limma package, but for that I need to > built my own CDF package, > probe package and built the filters to analyse one specie or another. > I'm using the makeProbePackage available in the AnnotationDbi (for a > R-2.13.0) but I got the following error message: > > Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument > > I already tried an old version of R-2.9.1 with a package matchprobes (that > is no longer update for R-2.13.0) > but the same error occurs. > > Does anyone knows how could I overcome this problem?Hi Helga -- Please ask this question on the Bioconductor mailing list, where you will get expert advice. http://bioconductor.org/help/mailing-list/ Be sure that your packages are up-to-date http://bioconductor.org/install/ and that you include the output of sessionInfo() in your post. Martin> Thank you very much for your attention. > Best Regards, > Helga > > >-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793