Re: [R] Correlation to a Single Gene

From: Charles C. Berry <cberry_at_tajo.ucsd.edu>
Date: Wed 17 Jan 2007 - 18:59:39 GMT

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
>
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>

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

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