hi,

I am trying to use the GeneSetCollection function to retrieve the BP GO 
gene sets over some Entrez genes.  But it seems like the ontology 
argument of GOCollection is not making a difference to which terms are 
in the resulting GeneSetCollection.  In the help for GOCollection it 
says " Unlike evidence code, ontology membership is enforced when 
GOCollection gene sets are constructed."  so I expected that the 
resulting object would only have BP GO terms.

thanks for any guidance,

a small example for the Entrez genes 1-20:

library(org.Hs.eg.db)
library(GSEABase)
gsc <- GeneSetCollection(as.character(1:20), 
idType=AnnotationIdentifier("org.Hs.eg.db"), 
setType=GOCollection(ontology="BP"))
table(unlist(eapply(GOTERM[names(gsc)],slot,"Ontology")))

  BP  CC  MF
101  26  44

 > sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] 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_2.7.1          GSEABase_1.20.0      graph_1.36.1
  [4] annotate_1.34.0      org.Hs.eg.db_2.8.0   RSQLite_0.11.1
  [7] DBI_0.2-5            AnnotationDbi_1.20.2 Biobase_2.18.0
[10] BiocGenerics_0.4.0   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] IRanges_1.16.4  parallel_2.15.0 stats4_2.15.0   tools_2.15.0
[5] XML_3.9-4       xtable_1.7-0

...also I tried for:

 > sessionInfo()
R Under development (unstable) (2012-11-01 r61067)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] GO.db_2.8.0          org.Hs.eg.db_2.8.0   RSQLite_0.11.2
  [4] DBI_0.2-5            GSEABase_1.21.0      graph_1.37.1
  [7] annotate_1.37.1      AnnotationDbi_1.21.5 Biobase_2.19.0
[10] BiocGenerics_0.5.1   Defaults_1.1-1       BiocInstaller_1.9.4

loaded via a namespace (and not attached):
[1] IRanges_1.17.13 stats4_2.16.0   tools_2.16.0    XML_3.95-0.1
[5] xtable_1.7-0

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