Dear All,
I have two matrices A (40 x 732) and B (40 x 1230) and would like to calculate correlation between them.  I can use: cor(A,B, method="pearson") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1) have more than 3 (or 2 or 1) corresponding mapping in B (mRNA, say, m1,m2,m3) and I would like calculate correlations between p1-m1, p1-m2, and p1-m3 and then for the second variable p2 etc. 
I have the mapping information in another file (annotation file). Could you please suggest me how to do that?
Thanks in advance.
Kind regards,Ezhil  
	[[alternative HTML version deleted]]

