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="" datab="" ase="" 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@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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