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). I am using R2.11.1 and affypdnn 1.22.0 for windows XP. 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]]