Thanks, that helped a lot. It took me less than 3 hours to perform the background correction.
Now I'm wondering if for the next step, quantile normalization, I could do a similar trick. Is there a way to precompute the target empirical distribution based on all arrays and then do the normalization on chunks of data (thus in an independent manner)? I can see the option targetDistribution under QuantileNormalization. Kind regards, Damian Plichta On Monday, February 17, 2014 4:03:54 PM UTC-5, Henrik Bengtsson wrote: > > Hi. > > On Sun, Feb 16, 2014 at 6:53 PM, Damian Plichta > <damian....@gmail.com <javascript:>> 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-af...@googlegroups.com<javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > 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.
