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+s789695n4078114...@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 > > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4078114&i=2>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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > http://r.789695.n4.nabble.com/Pairwise-correlation-tp4076963p4078114.html > To unsubscribe from Pairwise correlation, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4076963&code=bXVzYWhhc3NAZ21haWwuY29tfDQwNzY5NjN8LTE5ODYxNDM0OTI=> > . > NAML<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.InstantMailNamespace&breadcrumbs=instant+emails%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://r.789695.n4.nabble.com/Pairwise-correlation-tp4076963p4078915.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org 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.
