I suggest you post this on the Bioconductor list instead, as it would seem
much more relevant to your concerns.

-- Bert

On Mon, Jul 16, 2012 at 1:55 PM, Drinniol <drinniol@gmail.com> wrote:

> Hello, I am new to R and have a problem I have had some trouble with.
>
> Basically I have a list of some 80000 genes or so with data points for
> expression levels at various time points/conditions.  I also have subsets
> of
> these, usually only a few hundred genes in size, known to be associated
> with
> some biological process.
>
> What I want to do is correlate the entire list with my subset and then
> return out the gene names and correlations for correlations above a certain
> threshold - the idea being that these would be good candidate genes to look
> at more closely for possible interaction with said biological process.
>
> What functions should I use to correlate the subset to the whole set -
> keeping in mind that I need to keep track of gene names in both sets?  And
> how, then, from what I presume would be something like a 80000 x 200 sized
> matrix would I extract gene pair correlations over a certain threshold?  It
> would also probably be good if I could somehow remove the subset genes from
> the whole gene list before computation so as to avoid useless 1
> correlations.
>
> I'll keep trying on my own, but any help would be appreciated!
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Help-with-correlation-matrices-thresholding-tp4636697.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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