[R] suggestion for proportions

[array chip]

Hi, I am wondering if anyone can suggest how to test the equality of 2 proportions. The caveat here is that the 2 proportions were calculated from the same number of samples using 2 different tests. So essentially we are comparing 2 accuracy rates from same, say 100, samples. I think this is like a paired test, but don't know if really we need to consider the "paired" nature of the data, and if yes then how? Or just use prop.test() to compare 2 proportions?

Any suggestion would be greatly appreciated.

Thanks

John