[BioC] barcode with custom CDF

[Matthew McCall]

Dario,

Generating the barcode vectors (estimating the null distribution for
each probeset) typically isn't something one can run on a laptop. It
takes about 1-2 days running in parallel on about 20 nodes of a
computing cluster. If you have access to such resources, I'm happy to
help you create your own implementation. Is the custom CDF you're
using one of the Brain Array CDFs or something of your own design?

Best,
Matt


On Tue, Mar 26, 2013 at 7:03 AM, Dario Greco [guest]
<guest at bioconductor.org> wrote:
>
> Dear BioC-ers,
>
> I would like to run the function 'barcode' on a set of CEL files preprocessed with a custom CDF.
> I am wondering if there is a quick way to generate the needed vectors (mu and tau for the unexpressed distribution) in the same way as the package frmaTools allows for the fRMA necessary vectors.
> I hope I am not posting about an issue already treated in this mailing list, but searching it produced no obvious hints.
>
> thanks a lot for your help and suggestions.
> cheers
> dario
>
>
>
>  -- output of sessionInfo():
>
> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] hgu133plus2barcodevecs_1.0.5 hgu133plus2frmavecs_1.1.12
>  [3] hgu133abarcodevecs_1.0.5     hthgu133acdf_2.11.0
>  [5] AnnotationDbi_1.20.7         affy_1.36.1
>  [7] frma_1.10.0                  Biobase_2.18.0
>  [9] BiocGenerics_0.4.0           BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.30.2     affyio_1.26.0         Biostrings_2.26.3
>  [4] bit_1.1-10            codetools_0.2-8       DBI_0.2-5
>  [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7
> [10] IRanges_1.16.6        iterators_1.0.6       MASS_7.3-23
> [13] oligo_1.22.0          oligoClasses_1.20.0   parallel_2.15.3
> [16] preprocessCore_1.20.0 RSQLite_0.11.2        splines_2.15.3
> [19] stats4_2.15.3         tools_2.15.3          zlibbioc_1.4.0
>>
>
> --
> Sent via the guest posting facility at bioconductor.org.



-- 
Matthew N McCall, PhD
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Rochester, NY 14611
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