Hi, all; While analyzing Affymetrix data set, when gene-information is necessary after probe-level data analysis is performed, Bioconductor looks for a related CDF package and if it cannot find it locally, it tries to get it from Bioconductor web site and install it. (If this is not correct, please let me know.) My question is this. When Bioconductor tries to install CDF package, it tries to do it globally, I mean it requires some root-level security privilege to install the necessary CDF package. Is there any way that this can be done locally, that is make Bioconductor install the necessary CDF package in a user's local directory and fetch gene-information from it, which will not require root-level privilege? Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724

> please let me know.) My question is this. When Bioconductor tries to > install CDF package, it tries to do it globally, I mean it requires > some root-level security privilege to install the necessary CDF > package. Is there any way that this can be done locally, that is make > Bioconductor install the necessary CDF package in a user's local > directory and fetch gene-information from it, which will not require > root-level privilege? I'm not 100% sure of exactly how they handle things in affy to call the reposTools functions but I believe that the way you want to go about this is to put the directory that you wish to use .libPaths() to specify the directory you want the pacakges installed into. If you call '.libPaths(<dir>)', that will place the new directory in the front of your library path setting, and I believe that affy is taking the first one in that vector. -J