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: sheltons@stemcell.ucsf.edu


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