[BioC] CDF/Probe/Annotation for GNF1m custom chip

[Kasper Daniel Hansen]

On Apr 9, 2007, at 6:28 AM, James W. MacDonald wrote:

> Hi Cei,
>
> Cei Abreu-Goodger wrote:
>> Thanks for the reply Kasper.
>>
>> I now have cdf and probe packages for Mouse and Human GNF affy  
>> chips. Is
>> there some way I could contribute these to bioconductor?
>
> We only provide cdf and probe packages for commercially available Affy
> chips, specifically excluding custom chips. There are two reasons  
> for this:
>
> 1.) A custom chip implies that the chip was produced specifically for
> one (or a very small group of) researcher(s). Because these chips  
> won't
> be widely distributed, it doesn't make sense to spend the time and
> effort to maintain these packages.
>
> 2.) The cdf and probe packages for custom chips are not freely
> downloadable from Affy's website. We re-build the cdf and probe  
> packages
> for every release, so we have to be able to easily get the original
> source data. In addition, there may be legal issues concerning the
> ownership of the custom chip cdf and probe data that we don't want to
> get involved with.
>
> But thanks for the offer!

Is this also the case where someone offers to maintain the CDF  
package and the CDF package in question may have a large )at least  
larger than a single lab) audience (collaborating labs using the same  
chip). I think I will be in that situation "soon".

Kasper


> Best,
>
> Jim
>
>
>>
>> Cei
>>
>
>
> -- 
> 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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