On Wed, Mar 28, 2012 at 3:53 PM, Benton, Paul <hpaul.bento...@imperial.ac.uk> wrote: > Hello all R-er, > > I'm trying to run a resampling method on some data. The current method I have > takes 2+ days or a lot of memory . I was wondering if anyone has a better > suggestion. > > Currently I take a matrix and get the correlation matrix from it. This will > be called rho.A. Each element in this will be tested against the distribution > from the resampled correlation B matrix. > > Some example code: > > A<-matrix(rnorm(100), ncol=10) > B<-matrix(rnorm(100), ncol=10) > > rho.A<-cor(A) > > { > idx<-sample(1:10, 10) > idx > # [1] 8 4 5 7 1 9 2 10 6 3 > > rho.B<-cor(B[,idx]) > } ## repeat this x time (currently 500) > > ## in essence we then have the following : > rho.arrayB<-array(runif((10*10)*500), dim=c(10,10,500))
Err... no we don't. sample(10,10) ; sample(10,10) ... only permutes the columns, so the 500 cor(B) have exactly the same values in different off diag positions. Using runif they are unique > > ## Then test if rho.A[1,1] come from the distribution of rho.B[1,1] > pvalueMat[1,1]<-wilcox.test(rho.array[1,1,] , rho.A[1,1])$p.value > >From what I know cor(A)[ i , i ] = cor(B)[ j , j ] = 1 for any choice of A,B,i and j I don't think Wilcox intended his test to be used in this way.... I would start with fixing these issues first so you don't wait 2 days for a vector of NaN's Cheers > However, my array size would be 2300 x 2300 x 500 which R won't let me even > make as an empty structure. Any suggestion are more than welcomed !! > > Cheers, > > Paul > > ______________________________________________ > 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.