[BioC] GOstats with yeast2

Thu Jun 5 08:28:57 CEST 2008

Hi Sebastien,
   You could try to use the YEAST package (that seems to be the only one 
that is working, but it is going to be deprecated - so I will need to 
fix this in the next little while).

   From yeast2.db you can get ORFs (which is what will be used - mostly) 
in the YEAST package.  So once you map both the sig and uni IDs to ORFs, 
you can use those two vectors and set the annotation to "YEAST".

   Robert

Sebastien Gerega wrote:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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