n = 3420;
R = zeros(n,1);
P = zeros(n,1);
for j = 1:n
[R(j),P(j)]=corr(A(j,:)',B(j,:)');
end
If this is just a one-off thing with the dimensions of the data you've shown, then this will be fine. However, if you're dealing with larger data sets, or performing this calculation many times, you'll be better off calculating this yourself from first principles, rather than using the built-in functions:
k = 29;
dmA = A - mean(A,2);
dmB = B - mean(B,2);
stdA = std(A,1,2);
stdB = std(B,1,2);
R = mean(dmA.*dmB,2)./(stdA.*stdB);
tst = sqrt(k-2)*R./sqrt(1-R.^2);
P = 2*(1-tcdf(abs(tst),k-2));
On my machine, the loop version above takes about 0.3 seconds, whereas this "first principles" version takes 0.003 seconds.
