Given the assay is ok and the analysis is done correctly, the fact that the result would depend on the brand of chemicals one is using would invalidate all claims of the method beeing quantitative...

The performance of syber green is influenced by different factors including the brand of your thermocycler. 

To identify if your results are correct you must consider the background of your assays and put a negative control (which could be a mix without cDNA) to manage that background and calculate your real signal in your samples and housekeeping.

You should get similar values. You can run the same sample twice with the same reagents and you won't get the same exact fold-change. Hence why you use average values and SEM. 

thank you all for ur valuable answers..it was really useful.the average and SEM would take care of my variation and help me get significant results..