[R] pairwise correlations for large dataset

[Alayne L. Brunner]

Hello,

I need to calculate the correlation for all pairwise combinations in a very large matrix.  I have 25,000 elements and need to calculate the pairwise correlation with a different set of 5,000 elements.

I have written code that works, but it is extremely slow.  At the current rate, it will take a few weeks to finish running.  I'm looking for suggestions on performing the calculations more efficiently.

Here's what I currently have:

for (j in 1:dim(genes2)[1]){
	for(i in 1:dim(genes1)[1]){

 		 peak1<-as.vector(t(expression.data[genes1[i,1],]))
 		 peak2<-as.vector(t(expression.data[genes2[j,1],]))
 		
                 Cor.matrix[i,j]<-cor(peak1,peak2,method='s')
  }
} 


Thanks so much.

Alayne