<p>I had the same problem and the solution for it was to match the two arrays of MFCCs using the <a href="http://en.wikipedia.org/wiki/Dynamic_time_warping" rel="nofollow">Dynamic Time Warping</a> algorithm.</p>

<p>After computing the MFCCs you should now have, for each of your two signals, an array where each element contains the MFCCs for a frame (an array of arrays). The first step would be to compute "distances" between every one element of one array and every one element of the other, i.e. distances between every two sets of MFCCs (you could try using the <a href="http://en.wikipedia.org/wiki/Euclidean_distance" rel="nofollow">Euclidian Distance</a> for this). </p>

<p>This should leave you with a 2-dimensional array (let's call it "dist") where element (i,j) represents the distance between the MFCCs of the i-th frame in the first signal and the MFCCs of the j-th frame of your second signal.</p>

<p>On this array you can now apply the DTW algorithm:</p>

<ul>
<li>dtw(1,1) = dist(1,1)</li>
<li>dtw(i,j) = min (dtw(i-1, j-1), dtw(i-1, j), dtw(i, j-1)) + dist(i,j).</li>
</ul>

<p>The value representing the "difference" between your two files is dtw(n,m), where n = nr. of frames in the first signal, m = nr. of frames of the second one.</p>

<p>For further reading, <a href="http://arxiv.org/ftp/arxiv/papers/1003/1003.4083.pdf" rel="nofollow">this paper</a> might give you an overall view of applying DTW to MFCCs and <a href="http://www.psb.ugent.be/cbd/papers/gentxwarper/DTWAlgorithm.ppt" rel="nofollow">this presentation</a> of the DTW algorithm might also help.</p>
Matching two series of Mfcc coefficients
<p>I have extracted two series MFCC coefficients from two around 30 second audio files consisting of the same speech content. The audio files are recorded at the same location from different sources. An estimation should be made whether the audio contains the same conversation or a different conversation. Currently I have tested a correlation calculation of the two Mfcc series but the result is not very reasonable. Are there best practices for this scenario?</p>