I'm currently trying to compare the expression level of two different genes from fermentation samples, however I have had a lot of trouble in getting clean samples for the qPCR.
I use NO-RT and just Supermix, water, primer as controls.
In my most recent try my NO-RT and NTC samples showed Ct values at 37-52 (Im currently running around 60 cycles, not sure if thats to many (additional question?)). Can i neglect these values since they are fairly high? My samples are around 16-21 Ct. Or how would I check if these values have an impact on my samples? Do I need a positive control sinec I just want to measure the ratio between the two genes?