[BioC] Question regarding Affy SNP 5.0/BI_SNP arrays

Mayer, Claus-Dieter c.mayer at abdn.ac.uk
Thu Apr 30 11:03:29 CEST 2009

Dear all!

A collaborator asked me to help her with the analysis of some Affy SNP 5.0 arrays they obtained from the AGRE projecet (a huge database collecting many datasets concerning Autism Genetics).
I have to admit that I am pretty much a novice when it comes to SNP-arrays, so I started with taking a few cel-files and to see how I get on with them (learning by doing).

If I try to use the Bioconductor package oligo to read in the data files I get an error message saying "there is no package called 'pd.bi.snp", i.e. it seems that the program is looking for some annotation package other than the one usually used for the SNP 5.0 chips ("pd.genomewidesnp.5").

I opened the corresponding cel file in Notepad to check whether I am dealing with the wrong array type and compared it with example Affy5.0 files provided by Biconductor (which I could process without problem).

In the Bioconductor file it says "GenomeWideSNP_5.1sq" at some point, whereas in the identical position in the AGRE file it says "BI_SNP.1sq".
My conclusion is that for the AGRE arrays different chip definition files (CDF) are needed because their set-up is a bit different from a standard Affy 5.0 chip. I tried to find more about this googling but only found one link to a Dchip discussion group that didn't make me much wiser either (http://dchip.forum5.com/viewtopic.php?mforum=dchip&p=266).

So is there anybody out there who knows what a BI_SNP array is and what cdf file I have to use for it? At first glance neither Nettaffx nor the Bioconductor annotation packages seemed to give me an obvious solution.



 Dr Claus-D. Mayer                       | http://www.bioss.ac.uk
 Biomathematics & Statistics Scotland    | email: claus at bioss.ac.uk
 Rowett Institute for Nutrition & Health | or: c.mayer at abdn.ac.uk
 Aberdeen Universtity                    | Telephone: +44 (0) 1224 716652
 Aberdeen, AB21 9SB, Scotland, UK.       | Fax: +44 (0) 1224 715349
Biomathematics and Statistics Scotland (BioSS) is formally part of The Scottish Crop Research Institute (SCRI), a registered Scottish charity No. SC006662

The University of Aberdeen is a charity registered in Scotland, No SC013683.

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