[BioC] GOstats error

[Al Ivens]

Hi Sebastien,

I have had this problem before too.  It is due to the fact that some GO
terms are obsolete:

GO:0001584 rhodopsin-like receptor activity. OBSOLETE. A G-protein
coupled receptor that is structurally/functionally related to the
rhodopsin receptor. ...

As an interim work-around, I check the GO term annotations for each
locus being enrichment tested, and remove those GO terms that are not in
GO.db.

However, I am sure someone else will have a more elegant solution to
this problem!

Cheers,

al



> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Sebastien Gerega
> Sent: 02 September 2009 06:52
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] GOstats error
> 
> 
> Hi,
> Today I received the following error while using GOstats:
> 
>  > hgOver
> Gene to GO MF  test for over-representation
> 315 GO MF ids tested (15 have p < 0.01)
> Selected gene set size: 107
>     Gene universe size: 7005
>     Annotation package: lumiHumanAll
>  > summary(hgOver)
> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>   value for "GO:0001584" not found
> 
> Any idea what could be causing this? or the best way to work 
> around it?
> 
> Session info at the bottom.
> 
> Thanks,
> Sebastien
> 
> 
> 
>  > sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
> 
> locale: 
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1
> 252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=En
> glish_Australia.1252
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  
> methods   base     
> 
> other attached packages:
>  [1] GO.db_2.2.11             gplots_2.7.1             
> caTools_1.9              bitops_1.0-4.1          
>  [5] gdata_2.6.1              gtools_2.6.1             
> xtable_1.5-5             biomaRt_2.0.0           
>  [9] genefilter_1.24.2        KEGG.db_2.2.11           
> GOstats_2.10.0           graph_1.22.2            
> [13] Category_2.10.1          limma_2.18.3             
> lumiHumanIDMapping_1.2.1 lumiHumanAll.db_1.6.1   
> [17] GDD_0.1-13               lumi_1.10.1              
> RSQLite_0.7-2            DBI_0.2-4               
> [21] preprocessCore_1.6.0     mgcv_1.5-5               
> affy_1.22.1              annotate_1.22.0         
> [25] AnnotationDbi_1.6.1      Biobase_2.4.1           
> 
> loaded via a namespace (and not attached):
>  [1] affyio_1.12.0   GSEABase_1.6.1  lattice_0.17-25 nlme_3.1-93     
> RBGL_1.20.0     RCurl_0.98-1    splines_2.9.1  
>  [8] survival_2.35-5 tools_2.9.1     XML_2.5-1
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/biocondu> ctor
> Search the 
> archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>