[BioC] Problem with hyperGTest using ath1121501.db

[Ulrike Goebel]

Dear list,

I seem to have a problem with an obsolote GO id in  ath1121501.db.

 >paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, 
universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", 
pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ;
 >hgCondOver <- hyperGTest(paramsCondOver) ;
 > summary(hgCondOver)
Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
 value for "GO:0006118" not found       

The GO database release 2009-05-10 says "This term was made obsolete 
because it describes a molecular function." Having realized this, I 
removed all gene ids from both H3K27me3_BP and  uBP that had this term 
as sole annotation. But the error persists. (This is the only case where 
I had a problem with ath1121501.db's new capability of using AGIs -- 
normally it works fine !)

H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) 
identifiers. The lists are too long to post, but I could send them if 
needed.

 > sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GO.db_2.2.11         ath1121501.db_2.2.11 GOstats_2.10.0
[4] RSQLite_0.7-1        DBI_0.2-4            graph_1.22.2
[7] Category_2.10.0      AnnotationDbi_1.6.0  Biobase_2.4.1

loaded via a namespace (and not attached):
[1] annotate_1.22.0   genefilter_1.24.0 GSEABase_1.6.0    RBGL_1.20.0
[5] splines_2.9.0     survival_2.35-4   tools_2.9.0       XML_2.3-0
[9] xtable_1.5-5





-- 
  Dr. Ulrike Goebel
  Bioinformatics Support
  Max-Planck Institute for Plant Breeding Research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062 121