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
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