Greetings all, I have re-written my targets file recenty, in the context of an experiment whose gene expression was measured using Agilent single color arrays. Therefore, I ended up having to reload the files specified as my targets, carry out pre-processing again, run Limma etc. Preprocessing, however, is now giving my some headaches. _Apparently_, I have done nothing new compared to what I was doing just about 30 days ago. However, this is what I am getting now: > mappings=build.mappings(esetPROC,"hgug4112a.db") Loading required package: GO.db The mapping process takes a while ... Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Ontology", for signature "character" where > class(esetPROC) [1] "ExpressionSet" attr(,"package") [1] "Biobase" Here is a snapshot of my R installation > sessionInfo() R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.2.11 gplots_2.7.0 caTools_1.9 bitops_1.0-4.1 gdata_2.4.2 [6] gtools_2.5.0-1 hgug4112a.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 Agi4x44PreProcess_1.4.0 [11] genefilter_1.24.0 annotate_1.22.0 AnnotationDbi_1.6.0 affy_1.22.0 Biobase_2.4.1 [16] limma_2.18.0 loaded via a namespace (and not attached): [1] affyio_1.11.3 preprocessCore_1.5.3 splines_2.9.1 survival_2.35-4 tools_2.9.1 xtable_1.5-5 I am running the latest version of Agi4x44PreProcess which I installed today, just in case, via the Mac GUI, with dependencies. HTH to clarify what my problem is. Thank you, Massimo Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto