[BioC] Unable to get expression-values from cel-files of yeast

[James W. MacDonald]

Hi Roman,

Roman Brunnemann wrote:
> Hi.
> 
> I'm working with bioconductor since 2 month and I never had any 
> problems. I used CEL-Files from ATGenExpress and everything was okay.
>  Now I tried to analyse different CEL-Files of yeast. I used
> different sources (
> 
> http://chemogenomics.stanford.edu/supplements/01yfh/files/raw_data/tar_archives/
>  http://www.brownlab.info/publications/Brown2005/celfiles/index.htm )
> 
> 
> But I didn't succeeded to make an
> 
> library(affy) and than data <- justRMA() in the cel-file directory. 
> On two different machines I got two different errors. The first
> computer says:
> 
> ##########################
> 
> 
>> data <- justRMA()
> 
> Error in getCdfInfo(object) : Could not obtain CDF environment,
> problems encountered: Specified environment does not contain
> DNA_TAGS_3 Library - package dnatags3cdf not installed Data for
> package affy did not contain dnatags3cdf Bioconductor - dnatags3cdf
> not available

The problem here is that you need the DNA_TAGS_3.CDF file in order to
analyze these data. BioConductor only makes available those CDF files 
that are publicly available from Affy's website, and unfortunately this 
isn't one of them.

In order to analyze these data, you will need to do two things; first, 
you will need to find the DNA_TAG_3.CDF file (maybe you can get it from 
the Brown lab?), and second, you will need to build either a cdfenv or a 
cdf package using the makecdfenv package. See ?make.cdf.env for more 
information.

Best,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623