On 08/21/2010 12:19 AM, josquint wrote: > > I am running and analysis of sequencing data uisng the EdgeR package. I have > received the following error: > > Using grid search to estimate tagwise dispersion. Error: cannot allocate > vector of size 307.3 Mb > > indicating the memory allocation is too small. How would I change this > confiuration in R so that the script can run with the files I have? > > Help appreciated, Josquin
Hi Josquin edgeR is a Bioconductor package so please ask on that list. http://bioconductor.org/help/mailing-list/ You must be a subscriber to post. Adjusting memory allocation on Windows is an R FAQ http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021 Often the end answer is 'use a 64-bit Windows or Linux machine with more physical memory'. While the error says that you are running out of memory, my guess is that the function is being invoked incorrectly. To help diagnose the problem, please include the output of sessionInfo() and a code snippet (preferably directly reproducible by others) showing exactly what you are doing. The output of traceback() after the error occurs can be informative. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list 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.