[BioC] CDF and Annotation-GeneChip Porcine Genome Array

[James W. MacDonald]

Hi Ángeles,

Angeles Jiménez Marín wrote:
> To whom correspond,
> 
> My investigation group will use the GeneChip Porcine Genome Array. To 
> analyze the arrays results we need  the Chip Definition File (CDF) 
> and  the  annotation package but this Affymetrix chip is not listed on the 
> webpage http://www.bioconductor.org/data/metaData.htm.
> 
> I should like to apply for both documents to begin with our analysis as 
> soon as possible .

You can get the cdf using biocLite().

source("http://www.bioconductor.org/biocLite.R")
biocLite("porcinecdf")

There is no porcine annotation package, so you can do one of two things. 
First, you could use AnnBuilder to create your own annotation package. I 
haven't played with that package in a year or more, so I don't know how 
difficult that might be. In the past it was not straighforward to create 
packages for species other than human, mouse, and rat. Nianhua would 
know better than I.

Second, you could use the biomaRt package to annotate your data. You can 
either use biomaRt interactively to annotate a set of probesets, or you 
can use the functions in the affycoretools package that are designed to 
create HTML documents with annotation links.

Best,

Jim


> 
> Thanks in advance
> 
> Ángeles
> 
> 
> 
> 
> 
> Dra. Ángeles  Jiménez Marín
> Dpto. de Genética
> Campus Universitario de Rabanales
> Edificio C5, 1ª Planta
> 14071 CORDOBA
> SPAIN
> Tel./Fax : + 34 957 218730
> E-mail: gm2jimaa at uco.es
> 	[[alternative HTML version deleted]]
> 
> 
> 
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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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