On Wed, 17 Jan 2007, Damion Colin Nero wrote: > I am trying to find a way to perform pairwise correlations against one > gene in a matrix rather than computing every pairwise correlation. I am > interested in how 1 transcription factor correlates to every gene in a > matrix of 55 experiments (columns) by 23,000 genes (rows), performing > the correlation by rows. Trying to perform every pairwise correlation > in this fashion is too memory intensive for any computer I am currently > using so I am wondering if anyone had a method for doing pairwise > correlations to a single gene or if there is a preexisting package in R > that might address this.
You measure the transcription factor once in each of 55 experiments and you measure gene *expression* (or some other quantity) on each of 23000 genes? cor.vec <- cor (transfac, t( gene.mat ) ) will do. Questions like this might best be posted to the bioconductor mail list. > > Damion Nero > Plant Molecular Biology Lab > Department of Biology > New York University > > ______________________________________________ > R-help@stat.math.ethz.ch 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. > Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 ______________________________________________ R-help@stat.math.ethz.ch 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.