Hi Sam, I assume you mean that correlation for _genes_ (not samples) 11262:30000 is 0? I am the maintainer of the WGCNA package but unfortunately I don't have access to a Mac big enough to try 30000x30000 correlation matrix, but I would be thankful if you could try reproducing the problem with smaller matrices (e.g. 20000x20000) and try to produce a small reproducible example by generating the data using say rnorm, say like this:
nGenes = 20000 # as small as possible that still produces the error nSamples = 100 datExpr1 = matrix(rnorm(nSamples * nGenes), nSamples, nGenes) simMat = bicor(datExpr1, use = 'p') Best, Peter On Mon, Aug 19, 2013 at 11:53 AM, Shelton, Samuel <shelt...@stemcell.ucsf.edu> wrote: > Dear R developer, > > I am an R user and am currently having a problem with versions of R >3.0.0. > We build larger correlation matrices of >30000 with pairwise correlations > made. We have been using a line of code > > simMat=bicor(datExpr1,use="p") > > To build the similarity matrix with datExpr1 being a matrix with genes as > columns (>30000) and rows being samples. This code works fine on an iMac > running OSX 10.8.5 and using R 2.15.2 and the Rblas library. When I try to > run the same code with R version 3.0.0 and 3.0.1 it only partially builds the > matrix. It will return correlations for samples 1:11262 but from 11262:30000 > the matrix is full of 0's. > > We would like to be able to use R 3.0.0 to allow us to build larger > correlation matrices on our cluster but we can't use it at the moment due to > this problem. My colleague has previously had a similar issue when using snow > leopard and this was to do with a compatibility issue between snow leopard > and the veclib. Has something changed in version 3.0.0 to give an > incompatibility with the veclib? > > Many thanks > > Sam > > Samuel Shelton, Ph.D. > Postdoctoral Researcher, > The Oldham Lab, > The institute of Regeneration Medicine, > University of California San Francisco, > San Francisco, CA 94143 > > email: shelt...@stemcell.ucsf.edu > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
