As so have for so many before me, your suggestion worked like a charm. I just started a fresh R session and the process ran smoothly (took a few days, but my word was it satisfying!).
I cannot thank you enough for taking the time to help. Many many thanks, Jason Karamchandani On Sunday, August 26, 2012 8:03:16 PM UTC-4, Henrik Bengtsson wrote: > > Hi, > > I'm not sure what is going on. It should certainly not get stuck for > 14 hours, unless you're running out of RAM and you're swapping like > crazy, but that should not happen if you have, say, at least 1GB of > RAM. Are you doing this in a fresh R session? > > Where it seems to hang has nothing to do with the number of arrays; at > that stage it is only setting up/precalculating/caching annotation > data files. Try the following in a fresh R session: > > library("aroma.affymetrix"); > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6,Full"); > print(cdf); > ## AffymetrixCdfFile: > ## Path: annotationData/chipTypes/GenomeWideSNP_ > ## Filename: GenomeWideSNP_6,Full.CDF > ## Filesize: 470.44MB > ## Chip type: GenomeWideSNP_6,Full > ## RAM: 7.18MB > ## File format: v4 (binary; XDA) > ## Dimension: 2572x2680 > ## Number of cells: 6892960 > ## Number of units: 1881415 > ## Cells per unit: 3.66 > ## Number of QC units: 4 > > getFileSize(cdf) > [1] 493291745 > > getChecksum(cdf) > [1] "3fbe0f6e7c8a346105238a3f3d10d4ec" > > Do you get the same output? If so, then: > > ut <- getUnitTypes(cdf, verbose=-100); > > str(ut) > atomic [1:1881415] 1 1 1 1 1 1 1 1 1 1 ... > - attr(*, "types")= Named int [1:8] 0 1 2 3 4 5 6 7 > ..- attr(*, "names")= chr [1:8] "unknown" "expression" "genotyping" > "resequenc > ing" ... > > That getUnitTypes() call on this CDF takes 60 seconds on my notebook. > That's only the first time, then for all future calls on the same > machine it will pick up the cached results from file, so it'll only > take a fraction of a second. > > If it hangs here, something weird is going on with you setup. > > /Henrik > > On Tue, Aug 21, 2012 at 8:03 AM, CanadianJK <jkar...@gmail.com<javascript:>> > wrote: > > > > I have been trying to perform copy number analysis of SNP6.0 data. I am > unable to get past the "process" function, where R appears to hang (will > not respond to interrupt) after displaying the following line during the > verbose output from the process function call: > > > > 20120821 13:37:24| Reading types for *all* units... > > > > I thought this may just be taking a long time because of the size of the > dataset, but I reduced the dataset to just one .cel file and the problem > persists, even after letting it run for 14 hours or so. > > > > I am using aroma 2.5.0. > > I am running this on R Studio Server on a Bioconductor Amazon Machine > Image. > > > > function call: > > csC <- process(acc, verbose=verbose) > > > > All of the prior steps from the CRMAv2 vignette work smoothly. > > > > Any advice would be appreciated. > > > > jk > > > > -- > > 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/ > -- 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/