[BioC] Help with searching GO in R

John Zhang jzhang at jimmy.harvard.edu
Tue Oct 25 20:26:05 CEST 2005

>hello all, I am new to the list and new to R.  My goal is to look for 
ontologies that have to do with immune response and defense in the GO dealing 
with my microarrays.  I have created the lists with aafGO() function, and just 
don't quite know where to do from there.  Everytime i try to do a search or 
build a graph, R shuts itself down.  Any suggestions?  Thanks, Christina

Here is an example on how to get the probe ids on the HG-U 95Av2 chip 
corresponding to immune response and defense:

>goids <- unlist(eapply(GOTERM, FUN = function(x){
    if(Term(x) == "immune response" || Term(x) == "defense")
> probes <- mget(names(goids[goids]), hgu95av2GO2PROBE)
> all.probes <- mget(names(goids[goids]), hgu95av2GO2ALLPROBES)

Only immune response was found. Is defense a valid GO term?

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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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