Error: long vectors (argument 1) are not supported in .Fortran

Just to set the record straight, WGCNA is a CRAN package.

As to Ankush's question - the current WGCNA version does not support
analysis of more than about 46300 nodes (probes) in one block. You
have two options: 1. filter out some of the least-informative probes
(e.g., probes with lowest mean expression or lowest variance); 2. use
the "blockwise" approach as implemented in blockwiseModules. Set the
maxBlockSize argument to say 40000, and the function will
automatically split your data into 2 blocks and run the analysis in
each block separately.

The third option is to wait a few weeks (possibly months), I do have a
WGCNA update in the works that __should__ work on blocks larger than
46300.

Best,

Peter

On Fri, Feb 3, 2017 at 7:31 AM, Bert Gunter <bgunter.4567 at gmail.com>
wrote:

Probably wrong list. Try the Bioconductor list instead.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Fri, Feb 3, 2017 at 3:19 AM, Ankush Sharma <ankush.sak at gmail.com>

wrote:

Hi all ,

I'm working on WGCNA on  R-3.3.1 version to reconstruct gene -gene
coexpression networks of 54000 probes in 230 samples on Load Sharing
facility (Remote computing cluster). Despite memory at dispose, I'm
encountering a error of allocation of memory at soft thresholding step

or

 at TOM Similarity step.  The problem of memory allocation at soft
thresholding step  was corrected by allocating the required memory

using [bsub

-R "rusage[mem=40000]".

Error Message

 > # Turn adjacency into topological overlap

TOM = TOMsimilarity(adjacency);

Error in TOMsimilarity(adjacency) :

  long vectors (argument 1) are not supported in .Fortran

Calls: TOMsimilarity -> .C

Execution halted

Warning message:

system call failed: Cannot allocate memory


Is there a way to run build this TOMsimilarity matrix.


Thanks






Best Regards,
Ankush Sharma,PhD
Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7)
LISM, Institute of Clinical Physiology, Siena (Italy)
Experimental Oncology Unit (UOS),
I
nstitute of Clinical Physiology
- National Research Council,
 Siena (IT)

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