 # qRT-PCR: how to average multiple runs? - (Aug/19/2008 )

I am performing a relative quantification RT-PCR experiment with a gene of interest and a housekeeping gene in an experimental condition and a control condition. I ran all samples in triplicate. I have done the experiment three times. I have standard curves for both genes and I'm relating the gene of interest to the housekeeping gene. I'm then normalizing the experimental condition to the control condition. I am getting stuck with the math during the final step of trying to average the three experiments. Here's how I am proceeding.

I compare all samples to the standard curves to get an 'amount'. I then average the three replicates for each sample and get the standard deviation. I then divide the average for the gene of interest by the average of the housekeeping gene to get a relative amount. I propagate the standard deviation by multiplying the quotient by the sqrt of the sum of the squares of the CVs (st dev/mean).

I then normalize my experimental sample by my control sample and once again propagate the standard deviation.

That's all fine and dandy. The problem is that I did the experiment three times and I need to take the average of the normalized values. For instance, I have the following:
3 experiments (experimental/control): 1.1+0.1, 1.5+0.2, 0.9+0.05

How do I average these and propagate the errors? If I just ignore the errors and average then I would get 1.17+0.3, but since there is error in the amounts that I am averaging, don't I have to propagate them somehow?

thanks!

-kman42-

in this paper they talk extensively about comparing data from different runs and error propagation. its very helpful, even if you don't have the discussed analysis software.

-Ned Land-