I calculated the first PC1 (first eigenvector) of a Hi-C matrix. Some chromosomes look good, some others like the following one not:
In green, the first eigenvector. At the second layer, in blue, compartments B. In red, compartments A. Don't you thing there's too many compartments? I must say this is a sample with a knocked down gene. However, only few chromosomes look like this.
What do you think?