I can't see how it's stored like that and the email servers garble it up. Use dput() to create a plain text representation and paste that back in.
Thanks, Michael On Thu, Nov 17, 2011 at 9:37 AM, muzz56 <musah...@gmail.com> wrote: > Hi Michael, > Here is a sample of the data. > > Gene Array1 Array2 Array3 Array4 Array5 Array6 Array7 Array8 Array9 Array10 > Array11 Fth1 26016.01 23134.66 17445.71 39856.04 27245.45 23622.98 37887.75 > 49857.46 25864.73 21852.51 29198.4 B2m 7573.64 7768.52 6608.24 8571.65 > 6380.78 6242.76 6903.92 7330.63 7256.18 5678.21 10937.05 Tmsb4x 6192.44 > 4277.22 5024.59 4851.51 3062.55 4562.43 7948.1 5018.58 3200.17 2855.77 > 6139.23 H2-D1 3141.41 3986.06 3328.62 4726.6 3589.89 2885.95 7509.88 > 5257.62 4742.26 3431.33 5300.72 Prdx5 3935.7 3938.9 3401.68 4193.14 4028.95 > 3438.19 6640.15 5486.61 4424.57 3368.83 5265.92 > I want to retain the gene names in the data. What you've proposed will take > them out and I'll have to append them back to the results after the cor() > > On 17 November 2011 09:33, Michael Weylandt [via R] < > ml-node+s789695n4080177...@n4.nabble.com> wrote: > >> I think something like this should do it, but I can't test without data: >> >> rownames(mydata) <- mydata[,1] # Put the elements in the first column >> as rownames >> mydata <- mydata[,-1] # drop the things that are now rownames >> >> Michael >> >> On Thu, Nov 17, 2011 at 9:23 AM, Musa Hassan <[hidden >> email]<http://user/SendEmail.jtp?type=node&node=4080177&i=0>> >> wrote: >> >> > Hi Michael, >> > Thanks for the response. I have noticed that the error occurred during >> my >> > data read. It appears that the rownames (which when the data is >> transposed >> > become my colnames) were converted to numbers instead of strings as they >> > should be. The original header names don't change, just the rownames. I >> have >> > to figure out how to import the data and have the strings not converted. >> > Right now am using: >> > mydata = read.csv(mydata.csv, headers=T,stringsAsFactors=F) >> > >> > then to convert the data frame to matrix >> > mydata=data.matrix(mydata) >> > >> > Then I just do the correlation as Peter suggested. >> > >> > expression=cor(t(expression)) >> > >> > Thanks. >> > >> > On 17 November 2011 08:51, R. Michael Weylandt <[hidden >> > email]<http://user/SendEmail.jtp?type=node&node=4080177&i=1>> >> >> > wrote: >> >> >> >> On Wed, Nov 16, 2011 at 11:22 PM, muzz56 <[hidden >> >> email]<http://user/SendEmail.jtp?type=node&node=4080177&i=2>> >> wrote: >> >> > 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. >> >> >> >> Behold the great and mighty power that is R! Don't worry -- on a >> >> decent machine the correlation of a 2k x 2k data set should be pretty >> >> fast. (It's about 9 seconds on my old-ish laptop with a bunch of other >> >> junk running) >> >> >> >> > 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. >> >> >> >> This is a little worrisome: R carries column names through cor() so >> >> this would suggest you weren't using them. Were your headers listed as >> >> part of your data (instead of being names)? If so, they would have >> >> been taken as numbers. >> >> >> >> Take a look at dimnames(NAMEOFDATA) -- if your headers aren't there, >> >> then they are being treated as data instead of numbers. If they are, >> >> can you provide some reproducible code and we can debug more fully. >> >> The easiest way to send data is to use the dput() function to get a >> >> copy-pasteable plain text representation. It would also be great if >> >> you could restrict it to a subset of your data rather than the full 4M >> >> data points, but if that's hard to do, don't worry. >> >> >> >> You should have expected behavior like >> >> >> >> X <- matrix(1:9,3) >> >> colnames(X) <- c("A","B","C") >> >> cor(X) # Prints with labels >> >> >> >> Michael >> >> >> >> > >> >> > On 16 November 2011 17:11, Nordlund, Dan (DSHS/RDA) [via R] < >> >> > [hidden email] <http://user/SendEmail.jtp?type=node&node=4080177&i=3>> >> 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< >> >> >> >> . >> >> >> >> >> >> 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]] >> >> > >> >> > ______________________________________________ >> >> > [hidden email] >> >> > <http://user/SendEmail.jtp?type=node&node=4080177&i=4>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. >> >> > >> > >> > >> >> ______________________________________________ >> [hidden email] <http://user/SendEmail.jtp?type=node&node=4080177&i=5>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-tp4076963p4080177.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-tp4076963p4080194.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. > ______________________________________________ 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.
