Hello, I am new to R and have a problem I have had some trouble with. Basically I have a list of some 80000 genes or so with data points for expression levels at various time points/conditions. I also have subsets of these, usually only a few hundred genes in size, known to be associated with some biological process.
What I want to do is correlate the entire list with my subset and then return out the gene names and correlations for correlations above a certain threshold - the idea being that these would be good candidate genes to look at more closely for possible interaction with said biological process. What functions should I use to correlate the subset to the whole set - keeping in mind that I need to keep track of gene names in both sets? And how, then, from what I presume would be something like a 80000 x 200 sized matrix would I extract gene pair correlations over a certain threshold? It would also probably be good if I could somehow remove the subset genes from the whole gene list before computation so as to avoid useless 1 correlations. I'll keep trying on my own, but any help would be appreciated! -- View this message in context: http://r.789695.n4.nabble.com/Help-with-correlation-matrices-thresholding-tp4636697.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
