[BioC] GOstats with yeast2

[Sebastien Gerega]

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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>>
>