Hi, repost your question to the Bioconductor mailing list instead, and your chances for getting help will be much greater:
http://bioconductor.org/docs/mailList.html /Henrik On Tue, Jul 6, 2010 at 9:06 AM, Hasan, Ahmed Ryadh - hasar001 <ahmed.ha...@postgrads.unisa.edu.au> wrote: > Dear all, > I am a PhD student working with Affymetrix HGU133atag array for analyzing the > Latin square experiment. > > I was trying to generate gene expression index for hgu133atag array for PDNN > model. While extracting the chiptype specific data structure, I got the > following error- > > >> library(affypdnn) > Loading required package: affy > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > registering new summary method 'pdnn'. > registering new pmcorrect method 'pdnn' and 'pdnnpredict'. >> library(hgu133atagprobe) > Loading required package: AnnotationDbi >> energy.file <- system.file("exampleData", >> "pdnn-energy-parameter_hg-u133a.txt", package = "affypdnn") >> params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = >> "hgu133aprobe") > Calculating chip type specific parameters, (may take some time)... > | | > |Error in object$call : $ operator not defined for this S4 class >> > After this, I also tried to do it for hgu95av2 array as described in the > package manual- > >> library(affypdnn) > Loading required package: affy > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > registering new summary method 'pdnn'. > registering new pmcorrect method 'pdnn' and 'pdnnpredict'. >> library(hgu95av2probe) > Loading required package: AnnotationDbi >> energy.file <- system.file("exampleData", >> "pdnn-energy-parameter_hg-u95av2.txt", package = "affypdnn") >> params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = >> "hgu95av2probe") > Calculating chip type specific parameters, (may take some time)... > | | > |Error in object$call : $ operator not defined for this S4 class >> > Please help me to get rid of this error(Error in object$call : $ operator not > defined for this S4 class). > > Best regards, > > Ahmed Ryadh Hasan > > PhD Student, > Knowledge-Based Intelligent Engineering Systems centre (KES) > Mawson Lakes Campus, University of South Australia, > Mawson Lakes, SA 5095 > > Phone: +61 8 8302 8332 (Office) > +61 8 8359 5747 (Home) > +61 4 3006 4390 (Cell) > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.