search for: eigenstrat

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

...the question is, can I use the PCA data to correct my p-values (in single.snp.association) for population structure? In my real data, population structure is causing a lot of type I errors (false positive SNPs). I have read of some standalone software that does this sort of thing, for example EIGENSTRAT: http://www.biostat.jhsph.edu/~iruczins/teaching/misc/gwas/papers/price2006.pdf But I'd like to stick to R if possible. Any advice/comments welcome.

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a