[BioC] goTools: ontoCompare question

[davidl at unr.nevada.edu]

Hello,

     I ran ontoCompare on the full list of probes in the mouse4302 genechip both
with the default EndNodeList() and with a custom end node list containing only
the antioxidant activity, biological_process, cellular_component, and
molecular_function GO terms and found what appears to be a discrepency:

> length(sviData$svi$ID)
[1] 45101
> sviData$svi$ID[1:5]
[1] "1452670_at"   "1422340_a_at" "1452114_s_at" "1422644_at"   "1423359_at"
> listall<-list("allprobes"=sviData$svi$ID)
> endlist<-c("GO:0003674", "GO:0005575", "GO:0008150", "GO:0016209")
> totalAnnotations<-ontoCompare(listall, probeType="mouse4302", method="none")
> write.table(totalAnnotations, file="totalAnnotations.txt")
> totalAnnotations2<-ontoCompare(listall, probeType="mouse4302", method="none",
endnode=endlist)
> write.table(totalAnnotations2, file="totalAnnotations_reduced.txt")

When finding the total possible number of annotations for the top level GO terms
(BP, MF, CC), I got different numbers for the two approaches, but I got the
same numbers for "NotFound" and "antioxidant activity":

from totalAnnotations.txt
antioxidant activity	     127
biological_process	     2594
cellular_component	     2365
molecular_function	     2414
NotFound	             11120
...others

from totalAnnotations_reduced.txt
antioxidant activity	127
biological_process	28020
cellular_component	28509
molecular_function	30875
NotFound	        11120

I was just wondering if anyone knew why this might happen since it affects the
interpretation of a comparison I was going to do.  These data appear to reflect
the histogram output from ontoPlot (so I don't think its an R->txt->excel
thing).  Is the output with method="none" the total number of times all probes
are annotated at the endnode or at a child of the end node? Does it have
something to do with the "isa" values in EndNodeList() or my method of creating
endlist?

R v.2.5.0
goTools v1.8.0

Cheers,
Dave

--and thank you Dick for recommending topGO.  I found what I needed through that
package.