[BioC] Reporting results of HyperGTest

[Paolo Innocenti]

Hi all,

I performed two separate HyperGTest (pkg:GOstats) on different list of 
DE genes (trt1 vs control and trt2 vs control). The results are good and 
in the direction I was expecting: I can see from "htmlReport" that the 
GOterms overrepresented in each list support my hypothesis.

My problem now is to "quantify" and to "show" what I can see: I am 
looking for a nice way to format my results. I have around 50 GO nodes 
in each list, too many to list them all in two colums. Is there a 
graphical way (or a compressed table) to show differences in "which 
branches of the GO" are overrepresented, and possible overlaps?

I am basically looking for something in between htmlReport, a DAG graph 
and the function ontoCompare in goTools.

I appreciate any comments on this issue. I have no experience with DAG 
graph, so if you suggests that it is the way to go, I'd like to be 
pointed to some documentation (I found GOvis.pdf too confusing as a 
beginner)

Many thanks,
Paolo


-- 
Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden