<shameless plug>If you want to array analysis and cluster you might want to try dChip (http://www.dchip.org). It's not written in Perl and it runs on Windows but people seem to like it :-) (I didn't write it, but the guy who did is in my lab).</shameless plug>

Actually, we do a lot of microarray stuff (mostly Affy, some cDNA) using, among other things, Perl and R. Which affy files were you interested in parsing?