[BioC] barcode with custom CDF

[Dario Greco]

Dear Matt,
thanks a lot for the quick reply!
i'm working on data from 8 homo sapiens affymetrix platforms re-annotated with brainarray cdf (ensembl gene).
i can have access to relatively large computer clusters, so that is not worrying me.
the most obvious question is probably concerning what volume of data from chipsets other than 133a and 133p2 i would need in order to generate meaningful estimations.
thanks
d


On Mar 26, 2013, at 2:43 PM, Matthew McCall <mccallm at gmail.com> wrote:

> 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
> 112 Arvine Heights
> Rochester, NY 14611
> Cell: 202-222-5880