search for: genes2

...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