[BioC] CDF file for Rhodobacter

James W. MacDonald jmacdon at med.umich.edu
Fri Apr 22 22:41:03 CEST 2005

Yue Pan wrote:
> Hi all,
> I'm trying to use affy package to normalize (RMA normalization) the 
> intensity values in some ".cel" files for the species  /Rhodobacter 
> //sphaeroides. /However, I can not find the corresponding "CDF" file 
> from bioconductor web site. (i.e. the MetaData section does not contain 
> that species's CDF package.)

AFAIK, this isn't a commercially available Affy chip, so we don't have 
access to the CDF file. I would think that whomever you got the chip or 
chip data from would have the CDF, as this is part of the deal with a 
custom chip. I would suggest contacting them.

Once you have the CDF, you will need to make a cdfenv using the 
makecdfenv package. See ?make.cdf.env for more details.

If you wish to make an installed package, see ?make.cdf.package. Note 
that if you are on windows, you will need to get set up to install 
source packages before you will be able to use the results of this 
function. For this, see the R-FAQ for Windows #3.1. For further 
information about installing packages see 'Writing R Extensions' and  'R 
Installation and Administration'.



> Does anyone know where to get the CDF file for /Rhodobacter /or any idea 
> how to "RMA" normalize the .cel files for it?
> thanks,
> Yue
> /
> /
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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