[BioC] GOSemSim mgeneSim GO.BP calculation time

[Sandeep Amberkar [guest]]

Dear All,

I am using GOSemSim package to calculate semantic similarity of genes within a cluster, for all clusters derived from a clustering algorithm. I use the mgeneSim function to carry out these calculations. The function works fine for GO.MF and GO.CC ontologies but it seems to fail for GO.BP. When given a list of Entrez identifiers, the function seems to be stuck for a long time, thus requiring the R session to be terminated. No warning or error messages are produced. I don't seem to understand this behaviour of this function for GO.BP.. What could be wrong here? I would appreciate any help in this regard. Thanks a lot in advance.

Please find attached sample Entrez IDs used for the calculation and my R session info.

 -- output of sessionInfo(): 

Entrez ids = 1132,1147,1326,1540,1654,1831,1917,2058,2289,3301,3305,3310,3312,3313,3320,3326,3376,3476,3551,4790,4791,4792,4793,4794,5151,5495,5537,5646,5917,5966,5970,5971,5977,6885,7098,7128,7132,7185,7278,7763,8517,8518,8717,8737,8767,8915,9020,9253,9532,9701,9755,10010,10293,10318,10382,10454,10758,10848,10892,11035,11140,22870,23085,23118,23243,23291,23474,26133,26610,28511,28512,29110,29775,54765,55140,55250,55291,55728,57805,64170,64332,64343,79092,79155,81030,84433,89891,92609,113457,136319,148022,150684,203068,257397,347733,387521,387522

OS -- opensuse 12.1
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] org.Hs.eg.db_2.7.1   igraph_0.6-2         GOSemSim_1.14.0      BiocInstaller_1.4.7  AnnotationDbi_1.18.1
[6] Biobase_2.16.0       BiocGenerics_0.2.0   RSQLite_0.11.1       DBI_0.2-5           

loaded via a namespace (and not attached):
[1] GO.db_2.7.1    IRanges_1.14.4 stats4_2.15.1  tools_2.15.1  

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