Dear Christian, I am new to XPS and i would like to use it to analyse Mouse Gene ST arrays (MoGene ST arrays). However, XPS crashes my R session when trying to create a ROOT scheme file fore these arrays, and i don't know what may go wrong. Hopefully you can advise. :) Thanks, Guido What did i do? - I am using a windows machine (WinXP-SP3, 4GB memory) - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is there a way to check whether ROOT installed properly? - Then i downloaded the 'library' files', MoGene-1_0-st-v1.r4.pgf and MoGene-1_0-st-v1.r4.clf, and put them in a directory (D:\XPS\Affy\libraryfiles) - Next i downloaded the latest annotation files from Affymetrix (MoGene-1_0-st-v1.na29.mm9.transcript.csv and MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them according to your instructions here: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 45 87. The annotation files are in the dir D:\XPS\Affy\Annotation. - I also created a dir to save the ROOT scheme file (D:\XPS\CRAN\Workspaces\Schemes). When running XPS to create the scheme file R crashes... My lines of code: library(xps) libdir <- "d:/XPS/Affy/libraryfiles" anndir <- "d:/XPS/Affy/Annotation" scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" Below it crashes (line is from your previous referred post on the mailing list): scheme.mogene10stv1r4.na29 <- import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/")) Error message: Rgui.exe - Application error. The instruction at "0x002288931" references memory at "0x8d5056fc". The memory could not be "read". > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xps_1.4.8 > ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]