[BioC] Drosophila Genome build used for GeneChip Drosophila-2 CDF?

[Marc Carlson]

Hi David,

If your drosophila2 cdf package says it was made in 2008, then you are
using an old package (and possibly even an old version of R and
Bioconductor).  The most recently released package was made in October
of 2009.  And there will be another new one in the spring.

The Bioconductor annotations are updated every 6 months.  BUT, if
Affymetrix never updates their source materials, then our regular
updates will not be any more current for something like a cdf package. 
While Affy does seem to update a lot of their stuff we don't have the
resources to babysit them.  We simply get their very latest sources
whenever we rebuild these packages.  Unless you want to get into the
business of remapping probes, we are  all ultimately at the mercy of the
manufacturers for telling us what they mean and how they map. 

However, if you feel that the manufacturers claims about their product
are inadequate, the MBNI provides MANY alternative mappings for many
platforms.  They have done a lot of work on this stuff, so if you feel
inclined, I would encourage you to explore what they offer.

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp


  Marc




Dávid Molnár wrote:
> Hi Jim,
>
> thank you for the swift reply. I puzzled over that affymetrix
> datasheet before, and I should probably have been more specific on
> that: has affymetrix never updated this CDF based on Drosophila genome
> release 3.1? Is bioconductor using the unupdated affymetrix CDF?
> Release 3.1 of the Drosophila genome is from 2003.  Data and gene
> models have considerably improved since then. In the CDF packages on
> the bioconductor server the date of the files is from 2008. I
> speculated that somebody might have had a look on them recently. Is
> this true?
>
> Best regards,
> David
>
>
> 2010/1/12 James W. MacDonald <jmacdon at med.umich.edu>:
>   
>> Hi David,
>>
>> Look at the left margin here:
>>
>> http://www.affymetrix.com/support/technical/datasheets/drosophila2_datasheet.pdf
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> Dávid Molnár wrote:
>>     
>>> Dear all,
>>>
>>> I tried to find out in vain from which genome release the current Chip
>>> Description File for GeneChip Drosophila-2 was made.
>>> Could anybody give me please a hint?
>>>
>>> Best regards,
>>> David Molnar
>>>
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>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
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