[BioC] Is anyone using affylmGUI for Affy Exon 1.0 analysis?

[James W. MacDonald]

Hi Alan,

On 2/7/2012 10:43 AM, Alan Derr wrote:
> I'm trying to use the Bioconductor package "affylmGUI" to process some
> data from Affy Exon 1.0 chips. I get as far as loading the CEL files,
> but when I try to run normalization, I get following error: "Error in
> getCdfInfo(object): Could not obtain CDF environment, problems
> encountered: Specified environment does not contain HuEx-1_0-st-v2",
> followed by "Library - package huex10stv2cdf not installed..."

That's because affylmGUI uses the affy package for processing of the 
celfiles. You will be much better served by using either the oligo or 
xps packages to preprocess, and then use limma for differential expression.

If you insist on using affy, MBNI has a cdf package that you could use 
(a simple biocLite("huex10stv2_hs_entrezg") should get it for you). You 
will then need to change the annotation of your AffyBatch by hand to 
reflect the fact that you want to use this alternate cdf package. I am 
not familiar with affylmGUI, so don't know if there is an easy way to do 
that, or if you have to 'go under the hood' to do it.

Best,

Jim


>
> When I did a search on huex10stv2cdf, I found a link to (what looks
> like) the right file (huex10stv2cdf_1.15.0.tar.gz), but it's on a
> password-protected site. Any suggestions for where to find that file,
> or other suggestions on how to get this working?
>
> Eventually, I would like to process the data using limma...
>
>
> Alan Derr
> Verastem Inc.
>
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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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