> I'm still not sure if I should run through "ham" as well as "spam" or 
> not.  Is there a specific answer for this?

Yes you should run ham as well, because the Bayes algorithm needs to
compare againt both "spammy" and "hammy" words to determine how to
classify new mail. You cannot train it with only one kind! That would
be like just showing a bunch of differently coloured fruits to a child and
then hold up a potato and ask if it is a fruit. 

Kai

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