Re: [R] Principal component analysis PCA

2008-02-14 Thread Thomas Lumley
On Thu, 14 Feb 2008, SNN wrote: > > Thanks for the advice. > > I tried to find the cov of my matrix using R and it ran out of memory. How did you do this? The covariance matrix is only 115x115, so it shouldn't run out of memory cov(t(code)) should work If that doesn't work then tcrossprod

Re: [R] Principal component analysis PCA

2008-02-14 Thread SNN
> larger data sets where the entire data matrix doesn't fit in memory, you > need some sort of double loop. > > -thomas > > >> Zhaoming >> -Original Message- >> From: SNN [mailto:[EMAIL PROTECTED] >> Sent: Wednesday, February 13, 2008 9

Re: [R] Principal component analysis PCA

2008-02-14 Thread Thomas Lumley
d some sort of double loop. -thomas > 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 tryin

Re: [R] Principal component analysis PCA

2008-02-13 Thread Wang, Zhaoming (NIH/NCI) [C]
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

[R] Principal component analysis PCA

2008-02-13 Thread SNN
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=30) # do PCA # pr<-prcomp(code, retx=T, center=T) I a