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

[James W. MacDonald]

Hi David,

I guess it depends on what you are really after. The CDF simply maps the 
locations of the probes on a chip back to their probesets, so there is 
never any need to update that file (if Affy changed the design of the 
chip they would just release a new Drosophila chip as they did when they 
went to the Drosophila 2.0 chip).

I sort of assumed you originally meant to ask what genome build the chip 
was designed against, which is what they show in the pdf I directed you 
to. Again, this information is set in stone.

What may change is what the probes are assumed to bind to. If for 
instance an EST is later mapped to a particular gene, then the 
annotation for the probeset directed against the EST may change to 
reflect the newer annotation. These data are contained in the 
drosophila2.db package, which in turn is based on the most recent 
annotation file from Affymetrix. IIRC, Affy updates these annotation 
files quarterly, so we would have used the newest Affy annotation file 
as of October 2009 for the release version of this package.

Note that annotating the probesets is a non-trivial task, and we are 
simply taking the probeset -> Entrez Gene ID mappings from Affy and 
doing the mapping from Entrez Gene to the various other available 
annotation data. Since the annotation of any genome is a moving target, 
and it is a long time since 2003, some of the things that the probesets 
on this chip are intended to interrogate may no longer be interrogated 
as well (or at all), according to the genome as we now know it. Our 
annotation packages only take this into account to the extent that the 
annotation file from Affy does.

A different approach to this problem is taken by the folks at MBNI, who 
create their own CDF files based on the current genome build. If 
interested, you can see information about these packages at

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

They have set up a CRAN-style repository that biocLite() knows about, so 
if interested, you can get their packages directly using biocLite().

Best,

Jim



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.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues