The prefrontal asymmetry (FA) in the alpha band is a well-known physiological correlate of the emotional valence. Several methods for assessing the FA have been proposed in literature, but no studies have compared their effectiveness in a comprehensive way. In this study we first investigated whether the association between FA and valence depends on the computational methods and then, we identified the best one, namely the one giving the highest correlation with the self-reports. The investigated factors were the presence of a normalization factor, the computation in time or frequency domain and the cluster of electrodes used. All the analyses were implemented on the validated DEAP dataset. We found that the number and position of the electrodes do not influence the FA, in contrast with both the power computation method and the normalization. By using a spectrogram-based approach and by adding a normalization factor, a correlation of 0.36 between the FA and the self-reported valence was obtained.