If you pool the replicates you will get the same significance results for a 2x2 chi-square as for a t-test of the proportions.
A Mantel-Haenszel Test will make sure the replicates of a chi-square are not significantly different (there are other tests that do a similar thing).
Hi DRT, thanks. I've tried that before posting my problem here. And I just tried it again in case I have made a mistake previously. But even when I pool the samples (Treated: 78+ 482- and Non-treated: 403+ 2917-), and do a chi-square or Fisher's exact test, I got a p value of around 0.2. Have I missed something here?