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I am working on some genetic studies, where we are looking at the effects of each of 2.5 million genetic markers on multilevel models. I usually run my multilevel models on MLwiN or using runmlwin. But because of the number of models we run in these genetic studies, they have to be run on the high performance computer on a Unix platform. We were thinking about running the models on R, but the modelling options in R are not as flexible as those in MLwiN (e.g. you can only specify level 2 random effects, not level 1). Is it possible to run MLwiN on a Unix platform?

MLwiN does appear to run fairly well on Unix type systems if you run it with Wine (http://www.winehq.org/). We have recently updated our FAQs to provide some details on how to set this up (see http://www.bristol.ac.uk/cmm/software/m ... .html#unix).