[BioC] CDF for Cytogenetics_Array

[Sean Davis]

On Tue, Apr 27, 2010 at 8:03 AM, Lenka Radova <avodar at gmail.com> wrote:
> Hi,
> I have the original cdf file from Affymetrix web page
> (Cytogenetics_Array.CDF)  in my working directory and I tried the
> following... Lenka
>
>> library(makecdfenv)
>
>>  make.cdf.package("Cytogenetics_Array.cdf", cdf.path = getwd(), compress =
> FALSE, species = "Homo_sapiens")
> Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress,  :
>
>  makecdfenv does not currently know how to handle cdf files of this type
> (genotyping).

Hi, Lenka.

You'll want to use the oligo package, as Benilton suggested, to
process this chip type.  make.cdf.env is for 3' biased gene expression
arrays only, really.

Sean

>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
> locale:
> [1] LC_COLLATE=Czech_Czech Republic.1250  LC_CTYPE=Czech_Czech
> Republic.1250
> [3] LC_MONETARY=Czech_Czech Republic.1250
> LC_NUMERIC=C
> [5] LC_TIME=Czech_Czech Republic.1250
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> other attached packages:
> [1] makecdfenv_1.24.0 affyio_1.14.0     affy_1.24.2       Biobase_2.6.1
> loaded via a namespace (and not attached):
> [1] preprocessCore_1.8.0
>
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