I am having problems with my experiments on the 384 well block I am using, it seems inconsistant. When pippetting the exact same PCR mix (everything mixed into 1 tube) into random wells on the 384 plate, the result is variation in the fluorescence levels. However, the CPs dont seem to vary as much. There is no pattern as to which wells work better than others. One well might work great, then the well exactly next to it may fail to amplifly anything.
Is this likely a problem with my qPCR protocol conditions or is it a hard ware problem?