[BioC] GOstats error
Sebastien Gerega
seb at gerega.net
Wed Sep 2 07:52:00 CEST 2009
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.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_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
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