The model selection
for the Minimal Matrix
plus
Test
Dataset by cophenetic coefficient
analysis has been proposed by Monti et al.
2003 and used by Brunet et al.
2004 for NMF in the consensus
clustering framework. Although it does not
provide "binary" decisions" on the overall
clustering result (e. g. correct vs false),
the cophenetic coefficient
suggests which
models may be better than others In this case
k4, k12 and k14 appear to be overall reasonable
overall clustering results. Only k14 was chosen
for further downstream analysis, since the
resulting clusters resembled more our current
concepts of cell class identities than the more
comprehensive k4 clusters, allthough this will
be important to understand, on what basis these
4 clusters have been aggregated by sNMF. k12 was
not chosen, in order to have a "truly different"
results to compare with the Minimal Matrix
k12 results.