In the package genefilter, from www.bioconductor.org there is a function to do this (genefinder, if I recall correctly) best wishes Robert
Charles C. Berry wrote: > 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 >> >> ______________________________________________ >> [email protected] 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 > > ______________________________________________ > [email protected] 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. > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] ______________________________________________ [email protected] 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.
