[BioC] Problems creating CDF environment for Affymetrix SNP Array

[James W. MacDonald]

Hi Christoph,

On 12/14/2010 5:31 AM, Christoph Standfuß wrote:
> Hello, everyone
>
> I am currently analyzing 3 SNP arrays of type Affymetrix Mouse Diversity
> Genotyping Array. Unfortunately there is no CDF environment or
> annotation package available yet. So I tried to build an CDF environment
> on my own using make.cdf.env() function and the CDF file provided by
> Affymetrix library files.
>
> Calling
>
>  > MOUSEDIVm520650 <-
> make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF")
>
> I got the error message : "makecdfenv does not currently know how to
> handle cdf files of this type (ie not expression or genotyping)"
>
>  > traceback()
> 2: .Call("ReadCDFFile", file.path(path.expand(cdf.path), filename),
> PACKAGE = "affyio")
> 1: make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF")
>
>
> When I searched the internet for this error, I found an older message in
> this mailing list (http://bit.ly/fAYxOM), where it was mentioned, that
> "make.cdf.env is for 3' biased gene expression arrays only, really.".
>
> So my question is, if anybody of you could tell me how to deal with that
> problem or CDF file? I can't imagine, that I am the first guy facing
> that problem with this type of arry here?

You want to use the oligo package for this chip type.

Best,

Jim


>
>
>
> I tried R 2.10.* (bioconductor 2.5) and R 2.12 (bioconductor 2.7), but I
> had always the same problems.
>
> My sessionInfo() is
>
> R version 2.10.1 (2009-12-14)
> i686-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> Thanks for your help!
>
> Best regards,
>
> Christoph
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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