[BioC] error when using GOstats with AnnBuilder built package

[Marc Carlson]

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
>
>
>
>
>
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