Re: [R] Correlation to a Single Gene

From: Robert Gentleman <rgentlem_at_fhcrc.org>
Date: Wed 17 Jan 2007 - 19:17:45 GMT

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
>>
>> ______________________________________________
>> 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:cberry@tajo.ucsd.edu 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.
>
-- 
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
rgentlem@fhcrc.org

______________________________________________
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.
Received on Thu Jan 18 06:22:50 2007

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Wed 17 Jan 2007 - 20:30:30 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.