Hi karen,

I see 2 points that could explain these variations.

are you sure that your designed primers are specific to your control gene and did you test them to see if SNP are present in their sequences? If it's for "higher species", go to the UCSC website (http://genome-euro.ucsc.edu/index.html) and use the in-silico PCR. you'll be able to see in the genome browser with the appropriate tracks if SNP are present or not in your primers sequence.

the second point is the quality of each of your samples. poor RNA qualities affect largely amplification and therefore RTq-PCR results. different RNA qualities can give you therefore different results. You can assess this quality on machines as agilent bioanalyzer or simply by loading on agarose gels and see length patterns.

fred

In addition to Frederic's answer, of SNPs underlying the primers used and DNA quality. I just want to stress about DNA quality (run a 0.8% agarose gel at least to examine that). I also want to mention the most basic one of all: accurate estimation of DNA quantity (and that it is fully dissolved before measurement). This seems basic but often is overlooked.