[BioC] Error "Specified environment does notcontain MoGene-1_0-st-v1"

[Groot, Philip de]

Hello all,
 
Another (valid) way to still use the affy library is utilizing the MBNI Custom CDF-files:
 
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.asp <http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.asp> 
 
The libraries "mogene10stv1mmentrezgprobe" and "mogene10stv1mmentrezgcdf" are compatible with the affy-library, although normalization methods that utilize mismatch probes (like gcRMA and MAS5) won't work. If you apply normalization (e.g. rma or vsn), be careful with what you'll get.
 
So you can load the .CEL-files as follows (after installing these libraries):
 
library(affy)
x <- ReafAddy(cdfname="mogene10stv1mmentrezg")
 
Annotation libraries for the most popular MBNI Custom CDF-files can be found here: http://nugo-r.bioinformatics.nl/NuGO_R.html
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Wed 22/07/2009 08:48 PM
To: Peng Yu
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error "Specified environment does notcontain MoGene-1_0-st-v1"



Hi Peng,

Peng Yu wrote:
> Hi,
>
> I have some .cel files and MoGene-1_0-st-v1,r3.cdf in the current
> directory. The .cel files are generated from the Mouse Gene 1.0 ST
> Array.
>
> I run the following command. But it generate an error message. Can
> somebody let me know what the problem is?
>
> Regards,
> Peng
>
>> setwd(".")
>> library(makecdfenv)
>> data<-ReadAffy()
>> eset<-rma(data)
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-1_0-st-v1
> Library - package mogene10stv1cdf not installed
> Bioconductor - mogene10stv1cdf not available

Although the affy package can read these data in, it won't be able to
process the data without extra (unnecessary) work from you, as the affy
package wasn't designed to analyze these chips. Please see here:

http://www.bioconductor.org/docs/workflows/oligoarrays/

For a listing of packages that are designed for this chip.

Best,

Jim


>
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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