[BioC] problem with annaffy aafFunction function

[John Zhang]

>I am using annaffy to annotate some rat data. When using the aafFunction
>in affaffy, all of the objects returned were "character(0)". I then
>tried the function using the example code from the help page. I was
>surprised to get the same result. Is there a problem here? Session info,
>example code, and results below. Thanks. Mark

Yes, there is a problem but not on your side. The function tried to access the 
SUMFUNC environment of the annotation package. This element used to be available 
from LocusLink but we have not found the replacement yet after switching to 
Entrez Gene. That is why you did get anything useful.


>
>sessionInfo:
>
>R version 2.2.0, 2005-10-06, i386-pc-mingw32 
>
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
>"datasets"  "base"     
>
>other attached packages:
>  hgu95av2   annotate    rat2302 reposTools       affy    annaffy
>KEGG         GO    Biobase    RWinEdt 
>  "1.10.0"    "1.8.0"    "1.8.5"    "1.8.0"    "1.8.1"    "1.2.0"
>"1.8.1"    "1.6.5"    "1.8.0"    "1.7-3"
>
>Example code used:
>
>if (require(hgu95av2)) {
>         data(aafExpr)
>         probes <- geneNames(aafExpr)
>         functions <- aafFunction(probes, "hgu95av2")
>         show(functions[6:10])
>     }
>
>Results:
>
>An object of class "aafList"
>[[1]]
>An object of class "aafFunction"
>character(0)
>
>[[2]]
>An object of class "aafFunction"
>character(0)
>
>[[3]]
>An object of class "aafFunction"
>character(0)
>
>[[4]]
>An object of class "aafFunction"
>character(0)
>
>[[5]]
>An object of class "aafFunction"
>character(0)
>
>Mark W. Kimpel MD 
>
> 
>
>Official Business Address:
>
> 
>
>Department of Psychiatry
>
>Indiana University School of Medicine
>
>Biotechnology, Research, & Training Center
>
>1345 W. 16th Street
>
>Indianapolis, IN  46202
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084