Putting one group under more than one label

Hello all
Is there a way of labeling groups with more than one label? lets say I want to marge all of my samples from a specific groups to one group and compare them, something like all the samples from 2011 vs 2010, all the samples from treatment X vs Y. As consequence there is of-course an overlap, some of the samples would be in group X and group 2010 or 2011 and so on. Merge.groups tells me that the samples should be unique for a single group. Is there a way around that?