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. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Antonio Garcia-Martinez UC-Berkeley Physics/Joint Genome Institute http://cryptologia.com .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' ` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ______________________________________________ [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
