MATLAB: Getting rid of loops

Question

Hi, I am trying to clean matrix A (which is a 1064 x 4 matrix) while relying in the cleaning process on Matrices B and C that have the same size as A (Mat file attached). I developed a loop to clean A but I feel that a loop is unnecessary and that I can do it without relying on loops. Could the cleaning process be done much more efficiently? Your help is appreciated.

for i=1:size(A,1)
	for j=1:size(A,2)
		if A(i,j)<1 && A(i,j)>0 % this is the first issue in the cleaning process. A values between 0 and 1 should be equal to the respective value in matrix X
			A (i,j)=B(i,j);
		end
		if A(i,j)<C(i,j) % this is the 2nd issue I am facing A values lower than their respective C values are erroneous and should be replaced by NaN
			A (i,j)=nan;
		end
		if B(i,j)>100 %this is the third issue:  When B is greater than 100, A values should be equal to B values
			A (i,j)=B(i,j);
		elseif B(i,j)<0 %This is the fourth issue: negative percentages are missing observations
			A(i,j)=-999;
		end
		if C(i,j)==0%This is the 5th issue: when C is zero, A should be zero as well
			A(i,j)=0;
		end
	end
end

Answer 1

Logical indexing is much simpler than using loops:

idx    = A<1 & A>0;
A(idx) = B(idx);
A(A<C) = NaN;
idy    = B>100 | B<0;
A(idy) = B(idy);
A(C==0) = 0