I have run samples using two 96wells on two different run.

On the second plate i re-run two samples (6 replicates) as my inter-run control.

Now i have got the results and use qBASE to do inter-run calibration following the manual i just can proceed until i get the CF value (as attached file). So how do i normalize my second plate's Cq with the calibration factor to be comparable to the Cq Values of my first plate? any formula for it?

After reading for few time on Hellemans et al., Genome Biology, 2007., i realise that we need reference genes for normalization in order to do inter-run plate normalization (which i then realized qbase use "anonymous" as reference to normalize). However, i am now in the stage of choosing the best reference genes among the 7 house keeping genes that i am testing with three genes that are having inter-run "variation"( i assume).

Can i still do inter-run calibration? or are there other method or software to do?