[BioC] AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)

[Jenny Drnevich]

Updating may not solve your problem in this case - simpleaffy only has the 
control probe information for some common-used chips stored in it's 
environment; it doesn't take them from the cdf. There have been quite a few 
posts about this on the Bioconductor list... so many that it would be 
useful to put some sort of caveat in the help files for affyQCReport and 
simpleaffy! At any rate, check out my previous post and the possible fix 
referenced in it:

https://stat.ethz.ch/pipermail/bioconductor/2007-January/015575.html

Cheers,
Jenny

At 10:32 AM 2/6/2007, Seth Falcon wrote:
>Hi Emmanuel,
>
>"Emmanuel Levy" <emmanuel.levy at gmail.com> writes:
> > The reason is that the package of the chip I use (celegans) is not
> > found in .qcEnv
> >
> > Do you know why it is not added when I load the celeganscdf library?
> > Shall I add it myself? If yes could you please let me know how?
> >
> > Thanks in advance,
> >
> > Emmanuel
> >
> >> sessionInfo()
> > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu
>             ^^^^^
>
>That's a fairly old version of R (and hence you have rather old
>versions of the relevant BioC packages).
>
>Could you try updating to R 2.4.1, reinstalling BioC packages, and
>seeing if that resolves the issue?  If not, at least you will be a on
>a more up-to-date version and it will be easier for the developers to
>respond to your bug reports/feature requests.
>
>+ seth
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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e-mail: drnevich at uiuc.edu