[BioC] Question

James MacDonald jmacdon at med.umich.edu
Wed Jul 21 21:50:54 CEST 2004

You have to convert your soybean cdf to a cdfenv in order for affy to be
able to use it. The function to do this can be found in the makecdfenv
package on BioC, specifically make.cdf.env() and make.cdf.package(). The
former will make a cdfenv that you can use (and save) as an environment,
and the latter will make a package that will have to be installed before
you can use it (much like the packages available on the metadata page of

If you have problems making the cdfenv, you could send the cdf to me
(zipped of course) and I will make the package for you.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> <jcurry at vbi.vt.edu> 07/21/04 02:57PM >>>
I am using soychip data for R which unlike human etc is not
publicly available so it is not available in the metadata on
> I have it on my desktop, sent directly from affy.
> Being on the desktop, I thought that meant the cdf files were
> When I am attempting to read the data for the soybean file, I type
eset <- rma (Data)  and the error reads this:
> "Error in getCdfInfo(object) : Could not obtain CDF environment,
problems encountered:
> Specified environment specified did not contain Soybean
> Library - package soybeancdf not installed
> Data for package affy did not contain Soybean
> Bioconductor - soybeancdf not available"
> The soybeancdf has been installed into the affy library but it is
not on Bioconductor's website of packages available to download.  Is
this why it will not open?
> Any suggestions as to what I should do to rectify this problem?

Thank you.

Joyce Curry
Virginia Bioinformatics Institute, Virginia Tech
Bioinformatics 1 Washington Street
Blacksburg, VA 24061-0447

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