[BioC] goTools: ontoCompare question

[davidl at unr.nevada.edu]

Thank you Agnes,

     It makes sense to do it by the number of probes mapped to the GO instead of
the number of hits on it.  Thank you for the clear explanation.  I only have
one other question: Is the reason that molecular_function doesnt appear in the
list in your first example that the probe had already been mapped to an end
node below it in the list (i.e. binding, structural molecule activity,
transporter activity)?  I guess a more direct question is whether there are
more annotations at MF in my second example because I left out a lot of the
nodes under MF in that run (so the probes ended up contributing to MF and not
the end nodes that were children of MF).

Also, this is not directly related to my previous question, but do you think it
makes sense to divide the number of annotations at each node by the total
possible number of annotations at that node when using all 45101 probes on the
chip?  It seems like this would make it possible to compare the representation
of different end nodes in your probe set to each other (since some GO terms
have more children then others), but I feel like I may be missing something
about comparing end nodes to each other.

Thank you for the help,

Dave