On Fri, Dec 16, 2011 at 7:11 AM, Yuan Hao <yuan.x.hao@gmail.com> wrote:

> Dear list,
>
> I found "annotate::getAnnMap" seems not working for R-2.14.0.
>
> What I have is KEGG pathway ids, and I would like to return the pathway
> names using the following scenario commands:
>
> > library(Category)
> > keggID<-"04940"
> > getPathNames(keggID)
> Error: getAnnMap: package KEGG not available
>
>
Hi, Yuan.

This is not a bug, but the error message makes it sound worse than it
really is.  You'll just need to install the KEGG.db package.

http://bioconductor.org/packages/release/data/annotation/html/KEGG.db.html

Sean


> Also, the same Error message showed up when I try to use the 'summary()'
> function after "GOstats::hyperGTest". I would appreciate very much if it
> can be confirmed that this is a R/Bioconductor problem rather than a local
> one. Thank you very much in advance!
>
>
> > sessionInfo()
> R version 2.14.0 Patched (2011-11-25 r57751)
> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit)
>
> locale:
> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.**UTF-8/C/en_IE.UTF-8/en_IE.UTF-**8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] annotate_1.32.0       org.Hs.eg.db_2.6.4    limma_3.10.0
>  [4] affy_1.32.0           BiocInstaller_1.2.1   GOstats_2.20.0
>  [7] RSQLite_0.11.1        DBI_0.2-5             graph_1.32.0
> [10] Category_2.20.0       AnnotationDbi_1.16.10 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.22.0         genefilter_1.36.0     GO.db_2.6.1
>  [4] GSEABase_1.16.0       IRanges_1.12.5        preprocessCore_1.16.0
>  [7] RBGL_1.30.1           splines_2.14.0        survival_2.36-10
> [10] tools_2.14.0          XML_3.6-2             xtable_1.6-0
> [13] zlibbioc_1.0.0
>
> Cheers,
> Yuan
>
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