Averaging Multiple Magnitude Spectra I'm currently trying to implement some of the methods found in this paper on intelligent equalization - http://www.aes.org/e-lib/browse.cfm?elib=16792 - 

The first part of the process is to build a "target equalization curve" via the means of "averaging the spectra of all songs in the dataset".

In MATLAB, if I do the following.

mag_1 = abs(fft(file));
mag_2 = abs(fft(file_2));


The two magnitude spectra have different resolution and number of frequency bins right?  Does it make sense to just mean(mag_1, mag_2)?  I can't seem to find anything that goes over averaging multiple magnitude spectra and it isn't defined in the paper how they achieved the averaged magnitude spectra for the ideal target curve.

Any help would be appreciated.
If you're averaging multiple (two, in your case) spectral magnitude sequences your result will be valid, correct, as long as the sequences are equal in length.  Now whether the "averaged spectral magnitude" result gives you useful information, that you will have to decide on your own.