[BioC] Unique probes on all human affy chips

[Adaikalavan Ramasamy]

You have not told us what type of data you are looking for ? Do you want
the probe sequences, genbank identifiers or merely affymetrix ids ? Do
you know what Cel Definition File aka CDF is ? For brief explanation,
see http://www.bioconductor.org/data/cdfenvs/desc.html

I do not know how to do this in BioConductor. But if I need the
annotation information, I get it directly from affymetrix website. 

1) Select the human chip you want from 
http://www.affymetrix.com/support/technical/byproduct.affx?cat=arrays&Human
2) Find the section called "NetAffx Annotation Files" or "Sequence
Files" and select the format/file you want
3) At this stage you will be asked for login. Registration is free.

Suppose you have download the information of interest for all human
arrays, then you can remove redundancies by using the AffymetrixID which
is unique identifier of probesets. 



On Sun, 2004-09-19 at 15:59, S Peri wrote:
> Dear group, 
>  Is there any place where I can get all the unique
> probe ids for all the Affy human chips (~13 chips). 
> I am trying to get the unique probes (no duplicates).
> It turned out to be very computing intensive problem. 
> I took all the probes from all 13 chips and made a
> program that writes the the unique id (if there are
> duplicates, for e.g. 64474_g_at is there on HG-U95C,
> HGU133, HGU133A2, and 133_plus2. In this case my
> program will write 64474_g_at once in my output).
> Using c++ code it is running for the last 20 hrs. I
> made sure there are no bad loops that would put me in
> infinite loop situation. It would be nice to have all
> the uniqe ids in some place where i can use them
> directly for my annotation purposes. 
> 
> Thanks
> Peri.
> 
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