[BioC] GOstats with yeast2

[Sebastien Gerega]

Hi Robert,
at least the error wasn't from me doing something wrong!
can you think of any way around this problem? For example I could use 
GOstats with another yeast annotation DB but would then still have to 
map between affyID and some other type of identifier...
thanks,
Sebastien

Robert Gentleman wrote:
> Hi Sebastien,
>   I see, it seems that there are some issues in the GOstats/Category 
> packages for dealing with this that need a fair bit of attention.  I 
> am sorry to say that this is likely to take a few weeks for me to sort 
> out, but your report is most helpful.
>
>   best wishes
>    Robert
>
>
> Sebastien Gerega wrote:
>> Hi Robert,
>> here is the code I ran:
>> params = new("GOHyperGParams", geneIds=sig, universeGeneIds = uni, 
>> annotation="yeast2.db", pvalueCutoff=0.05, testDirection="over", 
>> ontology = "BP")
>> hgOver = hyperGTest(params)
>>
>> And I receive the following error:
>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>>  variable "yeast2ENTREZID" was not found
>> Error in mget(probes, ID2EntrezID(datPkg)) :
>>  error in evaluating the argument 'envir' in selecting a method for 
>> function 'mget'
>>
>> uni and sig contain affyIDs as follows:
>>
>> uni
>>   [1] "1769317_at"   "1769320_at"   "1769321_at"   "1769322_s_at" 
>> "1769333_at"   "1769336_at"   "1769342_at"   "1769350_at"   
>> "1769352_at"   "1769366_at"   "1769377_at"  [12] "1769388_at"   
>> "1769406_at"   "1769426_at"   "1769428_at"   "1769431_at"   
>> "1769443_at"   "1769446_at"   "1769450_at"   "1769455_at"   
>> "1769472_at"   "1769506_at"
>> etc etc.
>>
>> sig
>> [1] "1769579_at" "1769805_at" "1769955_at" "1770302_at" "1771153_at" 
>> "1771375_at" "1771705_at" "1772193_at" "1772642_at" "1772778_at" 
>> "1772785_at" "1773305_at" "1773699_at"
>> [14] "1773961_at" "1774540_at" "1774742_at" "1775014_at" "1775340_at" 
>> "1775851_at" "1775890_at" "1775925_at" "1776156_at" "1776550_at" 
>> "1776829_at" "1777569_at" "1777690_at"
>> [27] "1779266_at" "1779563_at"
>>
>> and finally:
>>  > sessionInfo()
>> R version 2.7.0 (2008-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252 
>>
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     
>> datasets  methods   base   other attached packages:
>> [1] GOstats_2.6.0        Category_2.6.0       genefilter_1.20.0    
>> survival_2.34-1      RBGL_1.16.0          annotate_1.18.0      
>> xtable_1.5-2         altcdfenvs_2.2.0   [9] hypergraph_1.12.0    
>> graph_1.18.0         Biostrings_2.8.0     makecdfenv_1.18.0    
>> GDD_0.1-12           annaffy_1.12.0       KEGG.db_2.2.0        
>> GO.db_2.2.0        [17] limma_2.14.0         affyPLM_1.16.0       
>> gcrma_2.12.0         matchprobes_1.12.0   affy_1.18.0          
>> preprocessCore_1.2.0 affyio_1.8.0         yeast2.db_2.2.0    [25] 
>> AnnotationDbi_1.2.0  RSQLite_0.6-8        DBI_0.2-4            
>> Biobase_2.0.0        yeast2cdf_2.2.0   loaded via a namespace (and 
>> not attached):
>> [1] cluster_1.11.10
>>
>> thanks for your help,
>> Sebastien
>>
>>
>> Robert Gentleman wrote:
>>> Hi Sebastien,
>>>   There is no requirement that I am aware of for ENTREZIDs. All that 
>>> is required is that you have some set of indentifiers (in this case 
>>> yeast standard names seem most likely) that map to KEGG. And 
>>> yeast2.db does seem to satisfy that requirement so I expect it would 
>>> simply work.
>>> Perhaps you could show what you tried, what happened and your 
>>> sessionInfo?
>>>
>>>
>>>   best wishes
>>>    Robert
>>>
>>>
>>> Sebastien Gerega wrote:
>>>> Hi,
>>>> what is the best way to use GOstats (specifically a hyperG test on 
>>>> KEGG) with the yeast2.db annotation? I have looked around the 
>>>> mailing list archive and the fact that yeast2.db doesn't have a 
>>>> yeast2ENTREZID environment has been mentioned several times. 
>>>> However, I haven't managed to find any mention of how to get around 
>>>> this and use the annotation with GOstats.
>>>> thanks,
>>>> Sebastien
>>>>
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>>>>
>>>
>>
>>
>