[BioC] affylmGUI and annotate problem?

James W. MacDonald jmacdon at med.umich.edu
Fri Feb 11 20:05:08 CET 2005

Anand C.Patel wrote:
> OK.  I have R 2.1 installed.  Have "all" of bioconductor installed.  Most
> everything works as expected, excepting that when I try to use affylmGUI, it
> works (including the GCRMA support, which is great), until the point where the
> probes are matched to the annotations.  At that point I get a string of error
> messages including:
> Error in mget(ls(cdfenv),env = mgu74av2GENENAME) :
> Object "mgu74av2GENENAME" not found
> It downloads the annotation files on its own, and does so successfully.
> What is causing this?

It's due to a change in how the annotation packages are being built that 
hasn't been completely resolved as yet. A simple solution is to paste 
the following code in your R session after you have attached the 
mgu74av2 annotation package.

files <- scan(file.path(.path.package("mgu74av2"),"data","filelist"), 
files <- as.list(sub("\\.rda$", "", files[-1]))
myEnv <- as.environment("package:mgu74av2")
data(list = files, envir = myEnv)

Then you should be able to proceed as normal.



> Thanks,
> Anand C. Patel, MD
> Fellow, Pediatric Pulmonology
> St. Louis Children's Hospital
> acpatel at usa.net
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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