Troubles interpreting microarray - (Jan/20/2006 )

Hello all,

I am fairly new to microarrays. I am having difficulty interpreting data that I have retrieved from affymetrix b. subtilis antisense arrays. When I use two different programs (dchip and bullfrog), I receive different calls on various genes. Although some of the calls on the genes are similar, many of them are widely divergent.

How should I resolve this disagreement?

Also, does someone know of a program that they could recommend for my purposes?

Thank you,

Matt