Problem- fluctuating negative control


I have what sounds to me like a simple question that I just want to hear some opinions on. I'm trying to quantify changes in gene expression over time in a treated sample relative to an untreated sample of cells. I've got what look like significant results, but I'm unsure of how to proceed with the stats because my negative control values fluctuate over a 24 hour period (in duplicate runs the fluctuation is consistent).

My question is, is there any way I can normalize my treated sample results against a fluctuating negative control? I'm not sure if I'm asking this correctly; is there any way I can 'pretend' my negative control remains at the same level, say, 100%, even though it doesn't? My initial thought was to increase or decrease the treated sample results by as much as the negative control increased or decreased (i.e. I assume that if the negative went down 25% between timepoints, and I see a decrease of 50% in a treated sample during that same period, I attribute 25% of the change to the same factor that decreased the negative control, and 25% of it to the treatment).

Any advice would be appreciated; my last exposure to stats was as a second-year undergrad.