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...my issue which is explained in detail at the bottom of this exchange... me: The data from this simulation has to be processed at several stages of data processing so at some point I do have to have to make a dissimilarity matrix from this large matrix, as well as ones that I have filtered. appleguy: >>>Your matrix is too big; adding more memory, or killing off other >>>processes won't help. R is clearly not very smart when it comes >>>to dealing with large chunks of data, and you're running into a >>>fundamental upper limit on the amount of data...