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
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>
> > To post to this group, send email to
> > aroma-af...@googlegroups.com<javascript:>
> > To unsubscribe and other options, go to
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>
--
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.
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