Comment: FYI be careful which program you use to analyze data from Bio-Rad therm - and be careful of the advice Bio-Rad offers (Aug/21/2010 )
This is a comment, not a question--but I figured this might be a good place to share for posterity.
The software used to analyze data coming from the iCycler iQ qPCR thermocycler has some annoying bugs in it (having to do with relabeling wells post-run). When I bugged Bio-Rad for a solution, they recommended I use the more current and compatible iQ5 software, and gave me a copy of it. Awhile later I realized that the results were often substantially different between these two pieces of software. When I called Bio-Rad a second time about this, they told me that I should trust the results from the iCycler software more for the iCycler iQ derived data (without providing much more in the way of details)---too bad they didn't feel the need to tell me this the first time.
I suppose this helps make the argument to use third-party open algorithm software for analysis of qPCR data.
I hope this saves a few others the problems I had.
As an additional note, even exporting the "raw fluorescence data" from iQ5 versus iCycler software yields differing results.