[BioC] GOstats error

Sebastien Gerega seb at gerega.net
Wed Sep 2 07:52:00 CEST 2009

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.


 > sessionInfo()
R version 2.9.1 (2009-06-26)


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

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