[BioC] Sc03b_MR_v04 CDF package

[James W. MacDonald]

Hi Ludo,

Ludo Muller wrote:
> Hi all,
> 
> I have data from hybridizations onto the Affymetrix yeast tiling array
> (Sc03b_MR_v04) which I would like to analyze using Bioconductor. However
> the CDF package (sc03bmrv04cdf) for this array doesn't seem to be available
> from the bioconductor website. Can anybody tell me if it is available
> elsewhere or whom I could contact about creating this package?

There will probably never be such a beast, as that implies the usage of 
the affy package. Instead, you should be using the oligo package and 
pdInfoBuilder. For that you will need the CIF and BPMAP files from Affy, 
and something like

pkg <- new("AffyTilingPDInfoPkgSeed", version = "0.0.1", author = "You", 
email = "you at yours.com", biocViews = "AnnotationData", genomebuild = 
"thegenomebuild", bpmapFile = <name of bpmap file>, cifFile = <name of 
cif file>)

makePdInfoPackage(pkg)

And then install using R CMD INSTALL <the package name>. You don't 
mention your OS, so that might simply entail running the above at a 
terminal prompt (if on Linux), or if you are on Windows or MacOS, you 
will need to get set up to build packages. See the R FAQ for either OS 
for further info about that.

Best,

Jim


> 
> Cheers,
> 
> Ludo.
> 
> ---
> Ludo A.H. Muller, Ph.D.
> Dept. of Molecular Genetics & Microbiology
> Box 3020, Duke University Medical Center
> Durham, NC 27710, USA
> 
> Phone: +1 (919) 681-6781 or 681-6778
> Fax: +1 (919) 684-8735
> E-mail: ludo.muller at duke.edu
> Homepage: http://www.duke.edu/~mulle019
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662