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

[Ankush Sharma]

Many thanks for the prompt response.

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)

On Fri, Feb 3, 2017 at 11:02 PM, Peter Langfelder <
peter.langfelder at gmail.com> wrote:

> 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)
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
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> >> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

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