Try EIGENSTRAT http://www.nature.com/ng/journal/v38/n8/abs/ng1847.html
or use a subset of SNPs. Zhaoming -----Original Message----- From: SNN [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 13, 2008 9:14 PM To: r-help@r-project.org Subject: [R] Principal component analysis PCA Hi, I am trying to run PCA on a set of data with dimension 115*300,000. The columns represnt the snps and the row represent the individuals. so this is what i did. #load the data code<-read.table("code.txt", sep='\t', header=F, nrows=300000) # do PCA # pr<-prcomp(code, retx=T, center=T) I am getting the following error message "Error: cannot allocate vector of size 275.6 Mb" I tried to increase the memory size : "memory.size(4000)" but it did not work, is there a solution for this ? or is there another software that can handle large data sets. Thanks -- View this message in context: http://www.nabble.com/Principal-component-analysis-PCA-tp15472509p154725 09.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.
