Thanks to everyone who replied to my post, I finally got it to work. I am
however not sure how well it worked since it run so quickly, but seems like
I have a 2000 x 2000 data set. My followup questions would be, how do I get
only pairs with say a certain pearson correlation value additionally it
seems like my output didn't retain the headers but instead replaced them
with numbers making it hard to know which gene pairs correlate.

On 16 November 2011 17:11, Nordlund, Dan (DSHS/RDA) [via R] <
ml-node+s789695n4078114h81@n4.nabble.com> wrote:

> > -----Original Message-----
> > From: [hidden email]<http://user/SendEmail.jtp?type=node&node=4078114&i=0>[mailto:
> r-help-bounces@r-
> > project.org] On Behalf Of muzz56
> > Sent: Wednesday, November 16, 2011 12:28 PM
> > To: [hidden email]<http://user/SendEmail.jtp?type=node&node=4078114&i=1>
> > Subject: Re: [R] Pairwise correlation
> >
> > Thanks Peter. I tried this after reading in the csv (read.csv) and
> > converted the data to matrix (as.matrix). But when I tried the
> > correlation,
> > I keeping getting the error (x must be numeric) yet when I view the
> > data,
> > its numeric.
> >
>
> What does R tell you if you execute the following?
>
> str(x)
>
> Just because the data looks like it is numeric when it prints doesn't mean
> it is.
>
>
> Dan
>
> Daniel J. Nordlund
> Washington State Department of Social and Health Services
> Planning, Performance, and Accountability
> Research and Data Analysis Division
> Olympia, WA 98504-5204
>
>
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