[BioC] Question regarding Affy SNP 5.0/BI_SNP arrays

Mayer, Claus-Dieter c.mayer at abdn.ac.uk
Thu Apr 30 17:35:38 CEST 2009

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


> -----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")

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