[BioC] Problems creating CDF environment for Affymetrix SNP Array

Christoph Standfuß christoph.standfuss at inf.fu-berlin.de
Tue Dec 14 11:31:56 CET 2010

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.


 > MOUSEDIVm520650 <- 

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?

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)

  [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

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Thanks for your help!

Best regards,


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