[BioC] how to find the probe set ID using different CDF file?

[Groot, Philip de]

Hello,
 
I missed this email previously, but I have an answer (I guess).
 
First of all, the MBNI Custom CDF is a new annotation of the Affymetrix CDF, so the number of probes in a probeset might be different. Additionally, some genes that were present on Affy might be gone with the MBNI Custom CDF and vice versa. Nevertheless, if you want to find corresponding probesetIDs, I guess it is best to consider the probe packages: extract the probe sequences from the affy CDF and match them with the MBNI CDF. The matches give you one (or more!) probeset IDs / probeset. Manual verification / curation of the probeset assignments is required I guess.
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: Wolfgang Huber [mailto:whuber at embl.de]
Sent: Tue 6-4-2010 22:41
To: James Anderson
Cc: bioconductor
Subject: Re: [BioC] how to find the probe set ID using different CDF file?



Hi James

it seems that nobody has answered your question because it is too vague.
What exactly do you mean by "corresponding"? Once you figure that out,
it should also become clearer how to do it.

        Best wishes
        Wolfgang


James Anderson:
> Hi,
> 
> I have 10 marker probe sets identified using Affy CDF (Hg 133A array). How can I find the corresponding probe set ID in the data normalized with MNBI entrez CDF file?
> 
> Thanks,
> 
> -James
>
>
>      
>       [[alternative HTML version deleted]]
>
>
>
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--

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact