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
>>
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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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide
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> 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
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PO Box 19024
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rgentlem at fhcrc.org