Hi, I'm the first to test this package and I have some problems. 1.I have installed perl on windows ( vista).. 2 In my directory QC : I've ONE file : mydata_Avg.txt , files generated by Genome Studio with label as indicated in vignette : - Index - TargetID - <sn>.AVG Beta .... 3 Then , I have tested my code : #biocLite("amap") library(amap) #biocLite("methylumi") library(methylumi) #biocLite("HumMeth27QCReport") library(HumMeth27QCReport) Dir = "F:/QC" Dir2 ="C:/Program Files/R/R-2.12.0/library/HumMeth27QCReport/DemoData" HumMeth27QCReport(Dir2) 4 First OUT: > HumMeth27QCReport(Dir) Erreur dans file(file, "rt") : argument 'description' incorrect > QCRep(Dir) Erreur dans file(file, "rt") : argument 'description' incorrect 5 I test with Dir2 with DEMODATA > HumMeth27QCReport(Dir2) Erreur dans file(file, ifelse(append, "a", "w")) : impossible d'ouvrir la connexion De plus : Message d'avis : In file(file, ifelse(append, "a", "w")) : impossible d'ouvrir le fichier 'sample.txt' : Permission denied QUESTIONS: Have I forget a file which describe my experiment? Have I misunderstanding in the documentation of HumMeth27QC packages? Thanks for your help Greg Biostatistician Montreal My config: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252 LC_MONETARY=French_Canada.1252 LC_NUMERIC=C [5] LC_TIME=French_Canada.1252 attached base packages: [1] tcltk grid splines stats graphics grDevices utils datasets methods base other attached packages: [1] HumMeth27QCReport_1.0 WriteXLS_2.1.0 plotrix_3.0-2 gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 [7] gdata_2.8.0 gtools_2.6.2 Hmisc_3.8-3 survival_2.35-8 methylumi_1.4.0 amap_0.8-5 [13] Biobase_2.10.0 loaded via a namespace (and not attached): [1] cluster_1.13.1 lattice_0.19-13 [[alternative HTML version deleted]]

Dear Greg, first of all thanks for your interest in HumMeth27QCReport. Regarding the errors seems that one of the three files doesn't have the required columns. You checked only the AverageBeta file but to work the package need also the Control and the Sample file. The error with the DemoData is because you don't have the permission to read the folder. Change the folder permission or copy the files in an other flder. All the best, Francesco -- *Francesco Mattia Mancuso* - Bioinformatician at Bioinformatics Core Facility - Bioinformatician at Proteomics Core Facility CRG-Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Telephone: +34 933160202 francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> [[alternative HTML version deleted]]