[BioC] some experiences and some troubles with GraphAT package

[Maria Persico]

Hello,

I'm using GraphAT package to "measure" the congruency between an
experimental dataset and the metadata GO biological process.

my experimental dataset is small if compared with GO meta data.
The specie on which I'm working is Yeast(cerevisiae).

The important absumption with the method "getpvalue" of GraphAT package is
that the graphs that you want "compare" must have the same nodes(obviously
the number of edges should be different). If the 2 adj matrices you want
compare are different in size you get an error.

In my specific case, I created a subset of the big GO meta data file(in
this subset I had only the nodes that were present in the experimental
dataset) and I tried to remove from this subset only the edges that gave
as similarity measures, values of Dij<3.I had 109 edges of this kind.

So I did :

for(i in 1:109){
GgoPredYBPnew<-removeEdge(as.character(edges.to.delete$V1[i]),
as.character(edges.to.delete$V2[i]), GgoPredYBP)
  }

but the graph that I obtained was only of one edge smaller!!!

May somebody help me?

I would have also some other questions regarding this package:

how to use the information about the edge weights? for
example I want to consider as "common edges" between two graph only
the ones that have a certain values in their edge weights....

If the graphs that I want to compare have a different set of nodes (some
in common ), does some method could be developed to work directly only
with nodes in common?

thanks for your attention.


maria



Maria Persico
MINT database, Cesareni Group
Universita' di Tor Vergata, via della Ricerca Scientifica
00133 Roma, Italy
Tel: +39 0672594315
FAX: +39 0672594766
e-mail: maria at cbm.bio.uniroma2.it