[BioC] GOSim yeast

[Marc Carlson]

Hi Fred,

I can't speak to what is happening with GOSim:::getGOInfo.  But if you 
are using the most recent version of bioconductor, then you could also 
do this kind of lookup like this:

library(org.Sc.sgd.db)
ID = "YHR055C"
select(org.Sc.sgd.db, keys=ID, cols = c("GO","ENTREZID"), keytype="ORF")


    Marc



On 05/22/2012 05:31 AM, Fred Hoffman [guest] wrote:
> Hello,
>
> I'm trying to use GOSim with yeast but with no luck. The function
> "setEvidenceLevel(organism="yeast")" doesn't seem to work.
>
> Using the org.Sc.sgd.db library, I obtain a long list of GO terms for "856452"
>
> Yet, getGOInfo("856452") yields,
>
>    No GO information available for these genes!
>
> Any help would be greatly appreciated.
>
> Yours,
>
> Fred Hoffman
>
>   -- output of sessionInfo():
>
>
> ID = "YHR055C"
>> # get Entrez Gene ID
>> get(ID, org.Sc.sgdENTREZID)
> [1] "856452"
>
>> # get GO terms
>> get(ID, org.Sc.sgdGO)
> $`GO:0010273`
> $`GO:0010273`$GOID
> [1] "GO:0010273"
>
> $`GO:0010273`$Evidence
> [1] "IMP"
>
> $`GO:0010273`$Ontology
> [1] "BP"
>
> .
> .
> .
>> setEvidenceLevel(organism="yeast")
>> getGOInfo("856452")
> Error in getGOInfo("856452") :
>    No GO information available for these genes!
>> setEvidenceLevel(organism="org.Sc.sgd.db")
> [1] "->  retrieving GO information for all available genes for organism 'org.Sc.sgd.db' in GO database"
> [1] "->  filtering GO terms according to evidence levels 'all'"
>> getGOInfo("856452")
> Error in getGOInfo("856452") :
>    No GO information available for these genes!
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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