[BioC] Human 50k Xba1 Affymetrix arrays cdf file

[James W. MacDonald]

Hi Christophe,

Christophe Poulet wrote:
> 
> 
> 
> Hello,
> 
> 
> I want to
> study SNP arrays (Human 50k Xba1 Affymetrix) with Bioconductor, and I don’t
> really know how to do, when I want to execute my cdf files from Gtype, R answer me that I
> don’t have the 50k Xba1 package. I’ve search it on the bioconductor website,
> but I didn't find it.
> 
> 
> I think
> that I must create this package with the cdf file here, but I
> don’t know how to do, could you help me please?

You need to install the oligo and makePlatformDesign packages. They are 
still developmental packages, so if you are using some version of R less 
than R-devel, you need to set your repository:

repos <- "http://www.bioconductor.org/packages/2.0/bioc/"
install.packages(c("oligo","makePlatformDesign"), repos=repos, 
dependencies=TRUE)

On R-devel you can simply use biocLite().

You will also need the cdf file, the annotation file, and the probe 
sequence file, which can be downloaded from Affy's website. You can then 
make the PDEnv using makePDpackage(). You will then need to install it, 
instructions for doing so can be found in the R-FAQ (how can add-on 
packages be installed?) or in the OS-specific FAQs if you are on Windows 
or MacOS.

HTH,

Jim


> 
> 
> 
> 
> 
> 
> Best
> RegardsChristophe PouletLaboratoire de Cytogénétique, CHUUniversité de Liège, Sart Tilmanchristophe.poulet at hotmail.com
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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