On Thu, 14 Feb 2008, SNN wrote:
>
> Thanks for the advice.
>
> I tried to find the cov of my matrix using R and it ran out of memory.
How did you do this? The covariance matrix is only 115x115, so it
shouldn't run out of memory
cov(t(code))
should work
If that doesn't work then
tcrossprod(code)/300000 - tcrossprod(rowMeans(code))
might.
> I am
> not sure how to do double loop to create the covariace matrix? Also is
> doing prcomp( covariace matrix) the same as finding
> prcomp( original data ,matrix of snps)?
That's the point of the paper behind the EIGENSTRAT software, which is
worth reading. The eigenvalues are the same and the eigenvectors are
related. One way around gives the left singular vectors of the data
matrix, the other gives the right singular vectors.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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