Did you try xlsread() to read in the workbook? You say you want to "compare the numerical cells" but don't say what compare means to you.
Then, after that comparison (whatever that is), you say you want to "calculate the number of difference". To find out if one variable is different from another, you can use isequal() to compare the whole variable (matrix), or use ~= to compare each element individually, like
differenceMap = matrix1 ~= matrix2; % A binary map of where they are different.
Then to count the number of differences you can sum that map
numberOfDifferences = sum(differenceMap)
