R help - Feb 2008 - 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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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


--
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.

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