Thanks for looking into this for me.
I made a mistake with the version of Osx I was using it is actually 10.8.4
mountain lion. Interestingly it was doing the same on this particular iMac with
snow leopard and that was the reason that I upgraded it to mountain lion. I
found the same problem with
On 21/08/2013 15:00, Prof Brian Ripley wrote:
On 21/08/2013 13:45, peter dalgaard wrote:
On Aug 20, 2013, at 19:42 , Shelton, Samuel wrote:
Hi all,
Thanks for getting back to me. We would like to move over to v3.0.0
on our
cluster so that we can build matrices larger than 46300*46300 (limit
In case this is helpful, I don't see this issue on my Mac Pro with OSX
version 10.7.5. Details below.
> M <- matrix(1,23171,23171) ; diag(M) <- 0 ; range(colSums(M))
[1] 23170 23170
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8
On Aug 21, 2013, at 16:39 , peter dalgaard wrote:
>
> Likely. I'm not seeing it on the iMac/SnowLeopard, only on the MacPro/Lion.
> I'm upgrading the MacPorts R on the MacPro now to see whether it has issues
> too, but of course that reinstalls everything but the kitchen sink...
Whoops. I don
On Aug 21, 2013, at 16:00 , Prof Brian Ripley wrote:
> On 21/08/2013 13:45, peter dalgaard wrote:
>>
>> On Aug 20, 2013, at 19:42 , Shelton, Samuel wrote:
>>
>>> Hi all,
>>>
>>> Thanks for getting back to me. We would like to move over to v3.0.0 on our
>>> cluster so that we can build matrices
On 21/08/2013 13:45, peter dalgaard wrote:
On Aug 20, 2013, at 19:42 , Shelton, Samuel wrote:
Hi all,
Thanks for getting back to me. We would like to move over to v3.0.0 on our
cluster so that we can build matrices larger than 46300*46300 (limit in R
<3.0.0)
but so far we can't get things to
On Aug 20, 2013, at 19:42 , Shelton, Samuel wrote:
> Hi all,
>
> Thanks for getting back to me. We would like to move over to v3.0.0 on our
> cluster so that we can build matrices larger than 46300*46300 (limit in R
> <3.0.0)
> but so far we can't get things to work with R v3.0.0 and higher. I a
Hi Peter,
But this is still an issue bellow the old R limit. I just tried the same
with a matrix of 3*3 and I see the same problem. This never used
to happen with R v2.15.2 and we could regularly build similarity matrices
of 45000*45000. This behavior of filling up the bottom of the matri
Hi all,
Thanks for getting back to me. We would like to move over to v3.0.0 on our
cluster so that we can build matrices larger than 46300*46300 (limit in R
<3.0.0)
but so far we can't get things to work with R v3.0.0 and higher. I am
trying to trouble shoot at the moment and I am now thinking tha
Hi Samuel,
WGCNA currently does not support calculations with matrices larger
than the old R limit, and it will take some time to update it to
support the large matrices. Furthermore, WGCNA relies on other
functions (most notably hclust) that would have to be updated as well
to support long vector
On Tue, Aug 20, 2013 at 9:23 AM, peter dalgaard wrote:
> What is bicor()? From the WGCNA package? Perhaps the package is doing
> something incompatible with the long vector support in R 3.0.0. You need to
> report such queries to the maintainer.
The maintainer is reporting for duty :)
The ver
Hi Sam,
I assume you mean that correlation for _genes_ (not samples)
11262:3 is 0? I am the maintainer of the WGCNA package but
unfortunately I don't have access to a Mac big enough to try
3x3 correlation matrix, but I would be thankful if you could
try reproducing the problem with sma
On Aug 19, 2013, at 20:53 , Shelton, Samuel 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 >3 with pairwise correlations
> made. We have been using a line of code
>
> simMat=bicor(datExpr
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 >3 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 ma
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