[BioC] Correlating all pairs of genes in a gene expression matrix?

[Thomas Girke]

You can use the cor() function like this:

## Some example data set
y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep="")))

## Create correlation matrix
c <- cor(t(y), method="spearman"); 

## Convert to distances
d <- as.dist(1-c)


On Thu, May 07, 2009 at 05:27:21PM +0100, Dan Bolser wrote:
> Hi,
> 
> Once I have loaded an x by y gene expression matrix (x genes by y time
> points), how do I get a matrix of gene-gene correlation?
> 
> I'm looking for a speedy method rather than the method with the latest
> greatest clustering algorithm... although the latter would be great ;-)
> 
> 
> Thanks for any help,
> Dan.
> 
> 
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