[R] Very large matrices for very large genome

[Antonio Garcia]

Hello,

I am using R to look at whole-genome gene expression data. This means
about 27,000 genes, each with a vector of numbers reflecting expression at
different tissues and times. I need to do an all against all co-expression
calculation (basically, just calculate Pearson's r for every gene-gene
pair). I try to store the result of such a thing in a 27000x27000 matrix,
but r seems not to like allocating such a large beast. Any
recommendations?

I also rather want to then manipulate the all-against-all interaction
data, treating it as a graph with edge weighted by the r^2, eliminating
some edges, maybe even finding network motifs like cliques, etc., so
having it as a manipulable object in r presents some advantages.
Alternatively, I could print it out maybe (don't even know how to do that)
and then write script code in another language to manipulate it.

All advice welcome.

A.

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Antonio Garcia-Martinez
UC-Berkeley Physics/Joint Genome Institute
http://cryptologia.com

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