[BioC] Spot IDs for pedbarray Packages

[Marc Carlson]

Francesco Favero wrote:
> Hi,
> I've used a number of "annotation.db" packages related to manufactured chip
> (like Affymetrix or Agilent for example) of Custom arrays (like LAPOINTE
> ...) and they were perfect never had a problem.
>
> I prefer to use the .db packages (example
> hgug4112a.db<http://bioconductor.org/packages/2.1/data/annotation/html/hgug4112a.db.html>,
> LAPOINTE.db, hgu133a2.db<http://bioconductor.org/packages/2.1/data/annotation/html/hgu133a2.db.html>etc...)
> because I can transform the package in a MySQL database. Than I can
> add some tables, or with an R script I can easily make queries in the
> desired database.
>
> Anyway, now I need to use the pedbarrayv9.db (and v10); They are FHCRC Human
> Prostate PEDB cDNA Array.
>
> I found out that the probe_id in the database  look like F:206190...
> F:206194... etc.
>
> I have some data from GEO and they use PEDB Spot IDs. They look like
> P:6860...  P:6868.. etc.
>
> So I can't do any search in the database, and also I can't find information
> about such IDs.
>
> Does anybody know something about those IDs and if I can convert F:* in P:**
> ?
>
> Thank you very much.
>
> Best regards
>
> Francesco
>
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>
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>   

Hi Francesco,

I am not an expert on the design of this particular platform.  But I CAN 
tell you that the "P" and the "F" IDs on these platforms are NOT the 
same.  The "F" IDs are labeled as feature IDs, and it really looks like 
this is probably what you should be using if you want to get data out 
about one of the unique features on this platform.  From the information 
I have there seems to be a one to many mapping between "P" IDs and the 
associated "F" IDs.  The "F" IDs are the more specific ID type. 

You will need to contact the people who initially made this platform for 
more details on the correct usage of these different ID types however.


    Marc