[BioC] Prolems with AraGene 1_1 annotation

[James W. MacDonald]

Hi Hugh,

On 7/22/2013 10:58 AM, Hugh Shanahan wrote:
> Hi,
>         I'm trying to do some work on the AraGene 1_1 st plate and I have a
> problem with the annotation for it. If you go to the Affymetrix web page
> you can download the annotation for it and probe sets will be labelled with
> an eight digit id, e.g. 13334158. On the other hand when I read in the raw
> data then the CDF will label the probe sets using a more conventional
> Affymetrix naming convention e.g. Ara-322976_st This means we can do our
> analysis but it's impossible to match up the genes with the probe sets.
>
> Has anybody encountered this problem before ? Any solutions ?

It's not clear to me what you mean by 'the CDF will label the probe 
sets'. What CDF? Note that there isn't and hasn't been IIRC, a 
conventional CDF for this chip.

Are you saying that the scanner returns a celfile with the wrong IDs, or 
is this something that is happening within a BioC package?

Taking stabs in the dark, I might recommend you ensure that the scanner 
has the updated library file installed. I took a quick peek at the 
current file, and didn't see any Ara-xxxx_st probeset IDs.

If the problem is due to a BioC package, please send us the code you are 
using and the output from sessionInfo().

Best,

Jim


>
> All the best
> Hugh
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099