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....@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]] > > ______________________________________________ > R-help@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. ______________________________________________ R-help@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.
