Another Cytoscape quirk - when importing data, redundant pairs of interactions are usually - but not always - ignored. This is a problem when I actually want to see how many different sets of data produced the same interactions, so doing such a comparison may be a better job for Excel.

Cytoscape also has trouble importing VizMapper settings almost all the time. Sometimes importing the settings then saving and reloading the network irons out any bugs.

Edit: I figured out the problem with failure to recognize redundancy. Cytoscape ignores redundant entries if the interacting nodes are presented in the same order, so Node1 (pp) Node2 only gets added to the network once even if the data set includes it twice with different attributes, i.e. if Node1 (pp) Node2 from Data Set 1 and Node1 (pp) Node2 from Data Set 2 are both in the input file. If Node1 (pp) Node2 and Node2 (pp) Node1 are both in the input file, though, both interactions are retained despite just being the inverse of each other. A solution: import the attribute as an interaction type.