On Mon, Jan 6, 2014 at 1:34 AM, Hans-Ulrich <hans-ulrich.kl...@uni-muenster.de> wrote: > Hi Hernik, > > Clearing the cache as you suggested did the trick: > > >> clearCache(dirs="aroma.affymetrix", recursive=TRUE, prompt=FALSE) > > Calculation of the sets of pobes with common SNP nucleotide pairs took much > more time after clearing the cache and I finally got 6 groups + "missing" as > expected. There must have been some corrupt files in my cache.
Thanks for the follow up. I don't know how the *contents* of those cache files got corrupted (the files themselves were valid since that corrupt content got read in). I have never seen this before, but my best guess is that the ACS file was corrupt, an I/O error occured while parsing that, and/or you somehow got used a non-working version of the affxparser package. The reason for it being slow is that it had to reparse and rebuild the CDF structure and lots of other things, which are now saved in file cache and for quick access. The clearCache() call erased all of the aroma.affymetrix file cache, so you'll find that it needs to rebuild the cache also for other chip type - I though that was the safest thing to do. Cheers, Henrik > > Thanks again for your help! > > Best, > Hans-Ulrich > > > -- > -- > 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.
