
 
 hi,
well what you asked is the major problem of automatic classification that i am also trying to resolve this year in my project:
choose the number of nodes first (SOM) or to classify objects 2 by 2 and than depending on the most clearly groups observed, decide how much groups to take (hierarchical clustering)? And instead using "amap" u can use "GeneSOM" package for the first method and "cluster" for the second because they are more developped than "amap"
Well if this is your question i advise you to use both methods first the hierarchical than the SOM. But with R you have one major problem the graphic visualization so if you have problems with this there is programs specialy for classification like cluster for Eisen et al. and GENECluster (doing SOM) for Golub et al. and they are very fast algorithms.
So wish you luck and wish that is what you're asking for, because there are many different methods for classification not based only on algorithmie like these two methods but on statistics ....
Regards
Ramzi



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