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. Thanks, Claus ********************************************************************** **** 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.

Hi Claus-Dieter, The BI_SNP cel files are for GenomeWideSNP_5. These are probably CEL files generated by one of our early access customers or development partners prior to the creation of the final scanning library files which use the official GenomeWideSNP_5 chip type name. So in short, use the GenomeWideSNP_5 library files with these CEL files. You can use the tool apt-cel-extract (part of the Affymetrix Power Tools: http://www.affymetrix.com/partners_programs/programs/developer/ tools/powertools.affx) to change the chip type in the CEL file to GenomeWideSNP_5. Best, Alan Alan Williams | VP, Informatics | Affymetrix, Inc. 6550 Vallejo Street, Suite 100 | Emeryville, CA 94608 alan_williams@affymetrix.com<mailto:alan_williams@affymetrix.com> ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. [[alternative HTML version deleted]]

Dear Benilton! Thanks for your answer. I was aware that you can specify the package name. If I use the option 'pkgname="pd.genomewidesnp.5"' my R console crashes under windows and gives me endless error messages ("caught segfault: address Oxd, cause unknown" under Linux, while it all works fine with REAL SNP5.0 chips, so I assume that this is just the wrong package for these arrays or the other way around: these are not standard Affy SNP 5.0 arrays. The question was rather: does anybody know about a package called "pd.bi.snp" or about arrays requiring something like that or has any other idea what might be going on here? Best Wishes Claus > -----Original Message----- > From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > Sent: 30 April 2009 15:46 > To: Mayer, Claus-Dieter > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Question regarding Affy SNP 5.0/BI_SNP arrays > > Hi Claus, > > comment below: > > On Apr 30, 2009, at 6:03 AM, Mayer, Claus-Dieter wrote: > > > 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"). > > you can override this by using the argument 'pkgname' (assuming > 'pkgname' is installed), eg: > > theData = read.celfiles(list.celfiles(), pkgname="pd.genomewidesnp.5") > The University of Aberdeen is a charity registered in Scotland, No SC013683.