I found the solution of my own problem posted above. Though, thanks for your kind help. I will still appreciate different ways to solve it specially with hist(), and histc(). Here is my solution to this problem:
[r, c] = size(A);
y = zeros(r,c);
p = zeros(r,c);
for i = 1:c %Looping through the column.
for j = 1:r %Looping through the row in that that column.
y(j,i) = sum(A(:,[i]) == A(j,i)); %Compare each column of the matrix with the entries in that column.
p(j,i) = y(j,i)/r; %Probability of each entry of a column within that column.