Differential Display and minimizing false positives

[Doug Perkins]

     Hello,
        I am preparing to try differential display (dd) with treated and 
     untreated cells to look for differences in gene expression.  I have 
     performed two exact cell experiments in parallel where I have treated 
     the cells (experiment A consists of treated and untreated cells and B 
     the same).  My question is:  Do you think it is best (for minimizing 
     false positives) to perform dd on experiment A RNA with duplicates 
     (ie; dd with treated and untreated twice) or with experiment A RNA and 
     B RNA (the parallel experiment) ?  I guess I'm not sure if I should 
     stick with one set of RNA and perform dupes or use/compare RNA from a 
     different (parallel) experiment.  Any suggestions ?
                                                        Thanks,
                                                                Doug