[R] Correlation to a Single Gene

Charles C. Berry cberry at tajo.ucsd.edu
Wed Jan 17 19:59:39 CET 2007

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 

 	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
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Charles C. Berry                        (858) 534-2098
                                          Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://biostat.ucsd.edu/~cberry/         La Jolla, San Diego 92093-0901

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