[BioC] problems using cdfenv

[James W. MacDonald]

Georg Otto wrote:
> Dear bioconductors,
> 
> i have a problem that presumably concerns my cdfenv installation.

This not due to the cdfenv, but due to simpleaffy. Unfortunately 
simpleaffy is not set up to do qc on the zebrafish chips, which is what 
the error you get is indicating. For a list of chips that simpleaffy 
knows about, you can type '.nms' (without the quotes) at an R prompt 
after loading the simpleaffy package.

Best,

Jim


> 
> I use the zebrafish affymetrix gene chip, and I tried simpleaffy to get 
> some quality control measures. Getting the expression measures with mas5 
> seems to work fine, but
> 
>  > qc<-qc(x, x.mas5)
> 
> Gives me an error message:
> 
> Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about chip 
> type: zebrafishcdf
> 
> I installed the zebrafishcdf from the bioconductor website but i still 
> get the same error. Then I made the cdf environment myself using the CDF 
> file from Affymetrix and makecdfenv. Unfortunately there is still the 
> same error.
> 
> Is there something that I missed?
> 
> Best regards,
> 
> Georg
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109