Hi. On Fri, Sep 17, 2010 at 12:58 PM, Matt <matt.kowg...@gmail.com> wrote: > Hi Henrik, > > I am processing the data from the 270 HapMap samples on the SNP 6.0 > arrays using the CRMAv2 method. I wrote a script to follow the steps, > minus the plotting, outlined on > > http://www.aroma-project.org/vignettes/CRMAv2 > > It has been running for a week now without error. I have checked > the .Rout file and it is still running, but it says it is doing chunk > #622 of 1252, so only half-way. I wonder if there is a way I can run > this faster? Is it possible to break the 270 samples up?
Have a look at the how-to page on 'Improve processing time': http://www.aroma-project.org/howtos/ImproveProcessingTime Obviously it depends on your computer, but on a decent machine I would expect something like 5-10 mins per array. If you see more than say 15 min per array, you should definitely look into the above how-to page. The CRMAv2 algorithm was designed to be a truly single array statistical method, meaning it will give identical result is process each array independently and then merge or you merge and the process all in one batch. This is neat, because you can process samples as they are added to an experiment/project. Because of this you can also run CRMAv2 on multiple machines in parallel. Note that this is not case with CRMA(v1) or any other CN preprocessing methods out there. If you wish to take this approach, you might by the doCRMAv2() function useful. See page 'Block: doCRMAv2() / doASCRMAv2()': http://www.aroma-project.org/blocks/doCRMAv2 Hope this helps Henrik > > Thanks for your help. > > Matt > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
