Dear Dimitris, Thanks so much for the reply.
However I got this memory error,when I run it on my data (12.7Mb). Is there a way I can make the code more memory susceptible. My dataset can be found here: http://dpaste.com/57274/plain/ __BEGIN__ > data <- read.table("mydata.txt") > nofsamp <- ncol(data) > nofrow <- nrow(data) > > mat.data <- data.matrix(data) > corr <- cor(t(mat.data)) R(1294) malloc: *** mmap(size=3948052480) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug R(1294) malloc: *** mmap(size=3948052480) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Error: cannot allocate vector of size 3.7 Gb Execution halted __END__ - Gundala Viswanath Jakarta - Indonesia On Wed, Jun 18, 2008 at 4:39 PM, Dimitris Rizopoulos <[EMAIL PROTECTED]> wrote: > try this: > > mat.data <- data.matrix(data) > cor(t(mat.data)) > > > I hope it helps. > > Best, > Dimitris > > ---- > Dimitris Rizopoulos > Biostatistical Centre > School of Public Health > Catholic University of Leuven > > Address: Kapucijnenvoer 35, Leuven, Belgium > Tel: +32/(0)16/336899 > Fax: +32/(0)16/337015 > Web: http://med.kuleuven.be/biostat/ > http://www.student.kuleuven.be/~m0390867/dimitris.htm > > > ----- Original Message ----- From: "Gundala Viswanath" <[EMAIL PROTECTED]> > To: <[EMAIL PROTECTED]> > Sent: Wednesday, June 18, 2008 8:55 AM > Subject: [R] Howto Compute Pairwise Similarity/Correlation Matrix from aData > Frame > > >> Hi, >> >> I have the following 5 vectors. I wish to compute >> the pairwise Pearson Correlation matrix with this data.frame. >> Is there a compact way to do it? >> >> At the end I hope to create a heatmap out of this correlation matrix. >> >> __BEGIN__ >>> >>> data <- read.table("mydata.txt") >>> print(data) >> >> V1 V2 V3 V4 V5 V6 V7 V8 V9 >> 1 42.3 53.2 76.4 78.8 83.6 91.3 92.2 105.8 109.6 >> 2 6.8 9.7 12.7 13.1 14.6 16.3 17.2 17.9 18.1 >> 3 10.6 21.5 34.4 38.2 38.8 50.0 60.7 64.0 64.3 >> 4 215.3 227.4 227.7 245.0 257.2 260.0 269.8 287.3 340.2 >> 5 4.1 4.2 4.6 6.4 6.8 6.9 16.9 17.6 23.3 >> >> __END__ >> >> Currently I am stuck in constructing the very matrix itself from >> double loop. >> >> __BEGIN__ >> data <- read.table("GDS596_part1.txt") >> nofrow <- nrow(data) >> >> for (rwx in 1:nofrow) { >> print(data[rwx,]) >> for (rwy in 1:nofrow) { >> print(data[rwy,]) >> >> thecor <- cor(data[rwx,],data[rwy.], method="pearson") >> # not sure how to proceed from here. >> } >> >> } >> __END__ >> >> Please advice. >> >> - Gundala Viswanath >> Jakarta - Indonesia >> >> ______________________________________________ >> 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. >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > ______________________________________________ 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.
