Re: [R] Principal component analysis PCA

From: Wang, Zhaoming (NIH/NCI) [C] <wangzha_at_mail.nih.gov>
Date: Wed, 13 Feb 2008 21:32:15 -0500

 

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:s.nancy1_at_yahoo.com]
Sent: Wednesday, February 13, 2008 9:14 PM To: r-help_at_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

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Received on Thu 14 Feb 2008 - 02:40:25 GMT

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