[BioC] Rat Gene 1.0 ST CDF files

[James W. MacDonald]

Hi Cunye,

cunye qiao wrote:
> Hello Bioconductor list;
>  
>     I'm currently looking at some Rat Gene 1.0 ST arrays. I get an error when I try to rma normalize a data set of Rat Gene 1.0 ST cel files. The code is following:
>  
> library(affy)
> library(annotate)
> a1<- ReadAffy(filenames = my.filenames)
> rma(a1)
>  
> The error message produced by R is following:
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered:
> Specified environment does not contain RaGene-1_0-st-v1
> Library - package ragene10stv1cdf not installed
> Data for package affy did not contain ragene10stv1cdf
> Bioconductor - ragene10stv1cdf not available
>  
> My question is where to find the ragene10stv1cdf and how to obtain CDF environment? Thanks.

You don't want to analyze the chip using the affy package. Instead you 
want to use the pdInfoBuilder/oligo pipeline.

See here:

http://article.gmane.org/gmane.science.biology.informatics.conductor/18963/match=oligo+st

for an example of how to do things. You want to build the pdInfo 
package, install it, then use oligo to do the analysis.

Best,

Jim


>  
>  
> Cunye
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662