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





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