Power Spectrum analysis arbitrary length signals I have signals belonging to diseased and healthy samples recorded from multiple electrodes. These signals are taken monthly and are of arbitrary length (say 4-5 mins). I am planning to do a power spectrum analysis (comparison between healthy and diseased). Now to do this two methods come to mind.

Take the normalized power spectrum of the 4/5 min signal as it is and average it over the electrodes.
Divide the 4-5 min recordings to smaller (say 5 seconds) segments, obtain the normalized power spectrum of each segment, average it over all the segments, and finally average it over the electrodes.

which of the following methods would give a better analysis?
The answer depends on the statistical characterization of the signal. If the random EEG signal is stationary over when seen over 5 second cycles, then you are better off averaging over 5 seconds cycles. If not, then averaging over these 5 seconds cycles might not yield the best estimate. In that case better off averaging over the entire duration.