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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_DK.UTF-8;LC_IDE NTIFICATION=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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >