[BioC] GOSemSim with mgoSim results changed based on the order of input GO terms

[Matt McNeill [guest]]

Is this expected behavior for mgoSim?

I am attempting to compare two lists GO terms. Each list was generated in a different species. Thus, I am using the "Wang" method and averaging the results using BMA. I noticed that if the GO term list is re-ordered, then the value in the thousandths decimal place changes (0.00X). I have tried several iterations of this now with the same result. 

Thanks for any insight you can provide.

Matt

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] GOSemSim_1.20.3      AnnotationDbi_1.24.0 Biobase_2.22.0      
[4] BiocGenerics_0.8.0   RSQLite_0.11.4       DBI_0.2-7           
[7] Rcpp_0.11.1         

loaded via a namespace (and not attached):
[1] GO.db_2.10.1   IRanges_1.20.7 stats4_3.0.2  


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