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.langfel...@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.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. > [[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.
