how to compare the similarity of two groups?

I have two groups: A, B, each group has several samples, such as
a1,a2,...a8 in group A and b1, b2,...b8 in group B. and I have a set of
genes, I have these genes expression profiles for every sample in A and
B.

could anyone please tell me how to compare the similarity (distance) of
the two groups by the gene expression profiles of their samples?

I am considering using euclidean distance as the metric, but I do not
know what software and how can perform such analysis. The TIGR's GDM
can give you a intuitive pictures, distances are represented by colors,
however, if I can get a number of the average distance between two
groups, that will be great!
Thanks.

.

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