Dear All, has there been a change in how you build you own annotation with AnnBuilder to use with e.g. GOstats? I just reannotated our in-house spotted human oligo chip and got an error message when using GOstats. > hgOverCond <- hyperGTest(params) Error in do.call(paste(pname, "dbconn", sep = "_"), list()) : could not find function "hsOligo_dbconn" Apparently I noticed that all new packages end with ".db", what does this mean? I tried to search the help lists but found only one post but that was regarding a Illumina chip that you provide the package for, so no luck there... best regards, // Johan > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: sv_SE.UTF-8/sv_SE.UTF-8/C/C/sv_SE.UTF-8/sv_SE.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] AnnBuilder_1.18.0 XML_1.95-2 GOstats_2.6.0 [4] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 [7] RBGL_1.16.0 GO.db_2.2.0 graph_1.18.1 [10] impute_1.0-5 hsOligo_2.0.1 kth_1.2.1 [13] geneplotter_1.18.0 lattice_0.17-6 aroma_0.94 [16] R.io_0.37 R.graphics_0.42 R.colors_0.5.3 [19] R.basic_0.49 aroma.light_1.8.1 R.utils_1.0.2 [22] R.oo_1.4.3 R.methodsS3_1.0.1 limma_2.14.5 [25] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.2 [28] RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.10 [4] grid_2.7.0 [[alternative HTML version deleted]]

Yes, We now ask that you use the SQLForge code inside of AnnotationDbi to make annotation packages instead of AnnBuilder. The new annotation package will have the .db extension on the end that you are looking for. The .db extension means that this package will be based on a small internal sqlite database which will be created by the SQLForge code. We are in the process of phasing out the non-sqlite based Annotation packages whenever possible because the newer packages provide greater flexibility to end users. You can find a tutorial vignette for both AnnotationDbi and SQLForge here: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html Please write back if you have additional questions, Marc Johan Lindberg wrote: > Dear All, > > has there been a change in how you build you own annotation with > AnnBuilder to use with e.g. GOstats? I just reannotated our in-house > spotted human oligo chip and got an error message when using GOstats. > > > hgOverCond <- hyperGTest(params) > Error in do.call(paste(pname, "dbconn", sep = "_"), list()) : > could not find function "hsOligo_dbconn" > > Apparently I noticed that all new packages end with ".db", what does > this mean? I tried to search the help lists but found only one post > but that was regarding a Illumina chip that you provide the package > for, so no luck there... > > best regards, > > // Johan > > > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-apple-darwin8.10.1 > > locale: > sv_SE.UTF-8/sv_SE.UTF-8/C/C/sv_SE.UTF-8/sv_SE.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] AnnBuilder_1.18.0 XML_1.95-2 GOstats_2.6.0 > [4] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 > [7] RBGL_1.16.0 GO.db_2.2.0 graph_1.18.1 > [10] impute_1.0-5 hsOligo_2.0.1 kth_1.2.1 > [13] geneplotter_1.18.0 lattice_0.17-6 aroma_0.94 > [16] R.io_0.37 R.graphics_0.42 R.colors_0.5.3 > [19] R.basic_0.49 aroma.light_1.8.1 R.utils_1.0.2 > [22] R.oo_1.4.3 R.methodsS3_1.0.1 limma_2.14.5 > [25] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.2 > [28] RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.10 > [4] grid_2.7.0 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >