Hi. On Sun, Feb 16, 2014 at 6:53 PM, Damian Plichta <damian.plic...@gmail.com> wrote: > Hi, > > I'm processing around 5500 affymetrix exon arrays. The > RmaBackgroundCorrection() is pretty slow, 1-2 minutes/array. I played with > setOption(aromaSettings, "memory/ram", X) and increased X up to 100 but it > didn't have any effect on this stage of analysis.
If you don't notice any difference in processing time by changing "memory/ram" from the default (1.0) to 100, then the memory is not your bottleneck. > > Any way to speed the process up? If you haven't already, make sure to read "How to: Improve processing time": http://aroma-project.org/howtos/ImproveProcessingTime If you have access to multiple machines on the same file system, you can do poor mans parallel processing for the *background correction*, because each array is corrected independently of the others. You can do this by processing a subset of arrays per computer, e.g. dsR <- AffymetrixCelSet$byName("MyDataSet", chipType="HuEx-1_0-st-v2") dsR <- extract(dsR, 1:100) bg <- RmaBackgroundCorrection(dsS) dsC <- process(bg, verbose=verbose) Repeat on another machine with 101:200, and so on. When all arrays have been background corrected, you can move back to your original script - all arrays background corrected are already saved to file and will therefore not be redone. /Henrik > > Kind regards, > > Damian Plichta > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
