[BioC] using GOSim with yeast genes

[prsmra01 at uniroma2.it]

Dear list,
I cannot use getGeneSim() with yeast genes (the code in vignette works  
properly for me but the entrez ids in the provided examples are from  
human); actually the problem seems linked to the mapping "yeast  
entrezIDs-GOterms" as you can see by trying the chunk of code below:

library(org.Sc.sgd.db)
library("GOSim")
x <- org.Sc.sgdENTREZID
setEvidenceLevel(evidences = c("IMP","IGI","ISS","IDA","IEP","IEA"),  
organism="yeast", gomap=NULL)
calcICs()
#now I move the ICs file in GOSim/data
setOntology("BP", loadIC=FALSE)
filterGO(Rkeys(x))
filtering out genes not mapping to the currently set GO category ...  
===> list of  6199 genes reduced to  0
list()

> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-03-03 r48046)
x86_64-unknown-linux-gnu

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

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

other attached packages:
  [1] GOSim_1.1.5.4          corpcor_1.5.2          Matrix_0.999375-21
  [4] lattice_0.17-20        RBGL_1.19.2            mclust_3.1-10
  [7] cluster_1.11.12        topGO_1.11.1           SparseM_0.79
[10] graph_1.21.4           org.Rn.eg.db_2.2.6     org.Pf.plasmo.db_2.2.6
[13] org.Mm.eg.db_2.2.6     org.Hs.eg.db_2.2.6     org.Dm.eg.db_2.2.6
[16] annotate_1.21.4        GO.db_2.2.5            org.Sc.sgd.db_2.2.8
[19] RSQLite_0.7-1          DBI_0.2-4              AnnotationDbi_1.5.17
[22] Biobase_2.3.10

loaded via a namespace (and not attached):
[1] grid_2.9.0   tools_2.9.0  xtable_1.5-4

May you give me some suggestions?

Thanks for your attention,
Best,
Maria
-- 
Maria Persico, PhD. student
http://cbm.bio.uniroma2.it/~maria/
MINT database group
Universita' di Tor Vergata, via della Ricerca scientifica 11
00133 Roma, Italy
Tel +39 0672594315 (Supervisor's room)
Fax +39 0672594766
Mobile phone: +393479715662
e-mail maria.persico at uniroma2.it