[BioC] Problem with hgu133plus2.db package

[Martin Morgan]

Hi Morten --

Morten Hansen wrote:
> Hi Martin
> 
> Yes - my package is using a namespace.
> 
> Everything worked fine after adding your suggestions to the DESCRIPTION and NAMESPACE files.
> 
> I need all the info in the hgu133plus2GO2PROBE - I think...

I don't know what the function does, but I was supposing that you were
going to look at only a subset of the GO ids in the table, and then
perhaps you would subset the map using [, and perhaps mappedLkeys or the
 like to extract information

  mappedLkeys(hgu133plus2GO2PROBE[goids])

Basically, thinking that you only want a subset of the available
information, and that it would pay to get only the information you want.

Martin

> Which function from AnnotationDbi can you suggest to extract information with?
> 
> Br - Morten
> 
> ________________________________________
> Fra: Martin Morgan [mtmorgan at fhcrc.org]
> Sendt: 16. juni 2009 13:41
> Til: Morten Hansen
> Cc: bioconductor at stat.math.ethz.ch
> Emne: Re: [BioC] Problem with hgu133plus2.db package
> 
> Hi Morten --
> 
> Does your package have a namespace? Maybe you need to have
> 
> Imports: AnnotationDbi
> 
> in the DESCRIPTION file and
> 
> importMethodsFrom(AnnotationDbi, as.list)
> 
> in the NAMESPACE file. But is this really what you want to do? Maybe
> it's better to use the standard AnnotationDbi interface to extract just
> the information you're interested in, instead of making everything into
> a list?
> 
> Martin
> 
> Morten Hansen wrote:
>> I have a problem with the hgu133plus2.db package.
>>
>> Usually when I want to use the data from hgu133plus2GO2PROBE , I do the following:
>>
>>> a <- as.list( hgu133plus2GO2PROBE )
>> Works fine.
>>
>> Now I am making a package and need to do the same. When running a function inside the package that does the same as above I get the following error:
>>
>> Error in as.list.default(hgu133plus2GO2PROBE) :
>>   no method for coercing this S4 class to a vector
>>
>> I also tried using mappedkeys() as explained in the example in help, but I get the same error.
>>
>> I have tested it on a clean R and Bioconductor installation.
>>
>> Any suggestions?
>>
>> My sessionInfo():
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> x86_64-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_DK.UTF-8;LC_NUMERIC=C;LC_TIME=en_DK.UTF-8;LC_COLLATE=en_DK.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_DK.UTF-8;LC_PAPER=en_DK.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_DK.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] icmmUtils_1.0.0       biomaRt_2.0.0         hgu133plus2.db_2.2.11 annotate_1.22.0       annaffy_1.16.0        KEGG.db_2.2.11
>>  [7] GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4             AnnotationDbi_1.6.0   Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.98-1 XML_2.5-1    xtable_1.5-5
>>
>> Br - Morten Hansen
>>
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>