I'm trying to use the Bioconductor package "affylmGUI" to process some data from Affy Exon 1.0 chips. I get as far as loading the CEL files, but when I try to run normalization, I get following error: "Error in getCdfInfo(object): Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2", followed by "Library - package huex10stv2cdf not installed..." When I did a search on huex10stv2cdf, I found a link to (what looks like) the right file (huex10stv2cdf_1.15.0.tar.gz), but it's on a password-protected site. Any suggestions for where to find that file, or other suggestions on how to get this working? Eventually, I would like to process the data using limma... Alan Derr Verastem Inc.

Hi Alan, On 2/7/2012 10:43 AM, Alan Derr wrote: > I'm trying to use the Bioconductor package "affylmGUI" to process some > data from Affy Exon 1.0 chips. I get as far as loading the CEL files, > but when I try to run normalization, I get following error: "Error in > getCdfInfo(object): Could not obtain CDF environment, problems > encountered: Specified environment does not contain HuEx-1_0-st-v2", > followed by "Library - package huex10stv2cdf not installed..." That's because affylmGUI uses the affy package for processing of the celfiles. You will be much better served by using either the oligo or xps packages to preprocess, and then use limma for differential expression. If you insist on using affy, MBNI has a cdf package that you could use (a simple biocLite("huex10stv2_hs_entrezg") should get it for you). You will then need to change the annotation of your AffyBatch by hand to reflect the fact that you want to use this alternate cdf package. I am not familiar with affylmGUI, so don't know if there is an easy way to do that, or if you have to 'go under the hood' to do it. Best, Jim > > When I did a search on huex10stv2cdf, I found a link to (what looks > like) the right file (huex10stv2cdf_1.15.0.tar.gz), but it's on a > password-protected site. Any suggestions for where to find that file, > or other suggestions on how to get this working? > > Eventually, I would like to process the data using limma... > > > Alan Derr > Verastem Inc. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues