[BioC] barcode with custom CDF

Hooiveld, Guido Guido.Hooiveld at wur.nl
Tue Mar 26 16:15:25 CET 2013

Hi Matt,
Sorry to interfere with this specific discussion, but i would also be interested in your suggestions on potential alternative approaches.
The reason I am interested is because ideally I would like to apply a (your) barcoding approach for platforms that are less used compared to the HGU133 or MOE430 platforms, such as the HuGene and MoGene ST v1.x arrays.


-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Matthew McCall
Sent: Tuesday, March 26, 2013 15:59
To: Dario Greco
Cc: Bioconductor at r-project.org
Subject: Re: [BioC] barcode with custom CDF


For the barcode implementations in BioC, I used > 10,000 arrays from each platform. I doubt this amount of data is available for all 8 Affy platforms you're using. If you don't mind giving me a brief overview of your research goals for this project (not cc'ing the BioC mailing list if you're more comfortable with that), I might be able to provide some alternatives to a full barcode implementation.


On Tue, Mar 26, 2013 at 10:47 AM, Dario Greco <dario.greco at ki.se> wrote:
> 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

Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880

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