[BioC] GOstats with yeast2

[Robert Gentleman]

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
>>>
>>> _______________________________________________
>>> 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
>>>
>>
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org