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.4...@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....@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. ______________________________________________ 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.
