[R] Error: long vectors (argument 1) are not supported in .Fortran
peter.langfelder at gmail.com
Fri Feb 3 18:32:21 CET 2017
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
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.
> 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.
>> 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),
>> nstitute of Clinical Physiology
>> - National Research Council,
>> Siena (IT)
>> [[alternative HTML version deleted]]
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