On Sun, 11 Apr 2004 19:15:08 -0700 (PDT), you wrote: >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.
How long is that vector? Presumably shorter than 27000. >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? If you have fewer than 27000 cases, then the correlation matrix is not full rank, and could be summarized in much less space. For example, if you have 100 cases, then a 100x100 matrix will give the correlation structure, and a 26900x100 matrix would give the weights for the rest of the genes. (It's late, so I might wrong about this, but I don't think so.) To calculate those matrices, just pick the first 100 genes to use for the correlation matrix (assuming you get a full rank matrix that way), then regress each of the others onto those. Duncan Murdoch ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html