I have to convolve a set of data points (counts per channel) with another set of data points (also in counts per channel). Could you please give me an idea on how to even begin to do this? I would prefer not to have to do FFT (and inverse transform...) on it as I don't know how to do that, but I could learn if there's no other way.
To obtain the convolution of two sets of data you should use the formula of a discrete convolution. You may use special formula for this, but using FFT will be faster. The most common fast convolution algorithms use fast Fourier transform (FFT) algorithms via the circular convolution theorem.