Hi Christophe, Christophe Poulet wrote: > Thanks for your answer, I've download and install the "oligo" and > "makePDpackage", and the Zipfiles from Affymetrix with success, but R > send another error, like this: > > > > > > >> makePDpackage()affymetrix expressionError in basename(filein) : >> argument You can't just call makePDpackage() with no arguments. You have to explicitly tell the function what files to use to make your package because it can't just figure it out on its own. If you type ?makePDpackage at an R prompt it will show you information about this function. However, simply making the package is only half the battle. You will also need to install it, which is not a simple task for someone without computer knowledge. You will probably need to find someone local who does have computer knowledge to help you get set up to install packages, and possibly install it for you. Information on how to do so can be found in the R FAQ for windows under section 4.1. Best, Jim > > "designFile" is missing, with no defaultI tried to find what and > where was the design file but I failed to find it.I forget to tell > you that I am a Biologist who try to work on windows with RGui 2.4.0, > it might be important, because I haven't got Computer Knowledge. You > can find a word doc which contains what I have done on R. > > Could you tell me what to do, because I don't find this problem in > the R FAQs for windows.Thanks for your time.Best regards.Christophe > PouletLaboratoire de Cytog?n?tique, CHUUniversit? de Li?ge, Sart > Tilmanchristophe.poulet at hotmail.com > _________________________________________________________________ > Lancez des recherches en toute s?curit? depuis n'importe quelle page > Web. T?l?chargez GRATUITEMENT Windows Live Toolbar aujourd'hui ! > http://toolbar.live.com -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi Christophe, Note that using makePDpackage under Windows, you must have the tools for building R Packages under your OS. http://www.murdoch-sutherland.com/Rtools/ The link above describe how to set up your system for this. To build the PDEnv for the XBA array you need the following files: Mapping50K_Xba240.CDF Mapping50K_Xba240_probe_fasta Mapping50K_Xba240_annot.csv Once you have these files in one directory, start R and change the working directory to the one where the files are (you can do this via menu/file/change directory or using the command setwd() ). Then you can use the command: makePDpackage("Mapping50K_Xba240.CDF", "Mapping50K_Xba240_probe_fasta", "Mapping50K_Xba240_annot.csv", type="SNP") to create the package... Now that the package is create you should build and install it. Let me know if you need any further help. b ps: The following page may be helpful: http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html On Nov 3, 2006, at 10:19 AM, Christophe Poulet wrote: > Thanks for your answer, > I've download and install the "oligo" and "makePDpackage", and the > Zipfiles from Affymetrix with success, but R send another error, > like this: > > makePDpackage() > affymetrix expression > Error in basename(filein) : argument "designFile" is missing, with > no default > > I tried to find what and where was the design file but I failed to > find it. > > I forget to tell you that I am a Biologist who try to work on > windows with RGui 2.4.0, it might be important, because I haven't > got Computer Knowledge. You can find a word doc which contains what > I have done on R. > > Could you tell me what to do, because I don't find this problem in > the R FAQs for windows. > Thanks for your time. > Best regards. > > Christophe Poulet > Laboratoire de Cytog?n?tique, CHU > Universit? de Li?ge, Sart Tilman > christophe.poulet at hotmail.com > > > Lancez des recherches en toute s?curit? depuis n'importe quelle > page Web. T?l?chargez GRATUITEMENT Windows Live Toolbar > aujourd'hui ! Essayez-le maintenant ! > <r.doc>