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.
On 16 November 2011 14:32, plangfelder [via R] < ml-node+s789695n4077593...@n4.nabble.com> wrote: > On Wed, Nov 16, 2011 at 8:37 AM, muzz56 <[hidden > email]<http://user/SendEmail.jtp?type=node&node=4077593&i=0>> > wrote: > > Dear All, > > I am not familiar with R yet I want to use it to perform some task, > hence my > > posting here. I hope someone can help. > > I have a set of data, genes (rows) and samples (columns). I want to do a > > Pearson correlation on all the possible pairwise combinations of all the > > genes (2000). Does anyone have an idea of how to execute this in R? > > Put the expression data in a matrix called expression > > Then simply execute > > correlations = cor(t(expression)) > > If you have missing data, use > > correlations = cor(t(expression), use = 'p') > > HTH > > Peter > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4077593&i=1>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-tp4076963p4077593.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-tp4076963p4077773.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.
