From peter.langfelder at gmail.com  Tue Aug 20 18:43:48 2013
From: peter.langfelder at gmail.com (Peter Langfelder)
Date: Tue, 20 Aug 2013 09:43:48 -0700
Subject: [Rd] Problem with R >3.0.0
In-Reply-To: <CE37B7C1.17CFF%sheltons@stemcell.ucsf.edu>
References: <CE37B7C1.17CFF%sheltons@stemcell.ucsf.edu>
Message-ID: <CA+hbrhUsbQOA-qa3x27VfmbKTt19JCuDuzUMR8icxbxbB7OZ3Q@mail.gmail.com>

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
<SheltonS at 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: sheltons at stemcell.ucsf.edu
>
>
>         [[alternative HTML version deleted]]
>
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[Rd] Problem with R >3.0.0
Peter Langfelder