[BioC] make CDF env (fwd)

w.huber at dkfz-heidelberg.de w.huber at dkfz-heidelberg.de
Fri Mar 28 18:01:08 MET 2003

Hi Wenqiong,

since you seem to use the package "makecdfenv" from the "Developmental
Packages" section, please also use a recent version of "Biobase" from
there. The function "createPackage" is in there.

For the use of the make.cdf.env function, please see the vignette. You
need to make sure that the returned data from this function is stored by R
in a place where the affy library can find it (namely, in an "environment"
of the name XXXXXcdf.

Best regards

Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany

On Fri, 28 Mar 2003, Rafael A. Irizarry wrote:

> i havent had time to look at the new makecdfenv. *if* you answer her can
> you cc me?
> ---------- Forwarded message ----------
> Date: Thu, 27 Mar 2003 12:10:49 -0800
> From: Wenqiong Chen <jchen at diversa.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] make CDF env
> Hi, I am a new user of BioConductor, and am currently working on Affy data
> analysis. I am trying to set up my own CDF package using the "makecdfenv"
> package. Here are the problems:
> -> Assuming that I have loaded the "makecdfenv"  library, and stored the
> .CDF file in my current working directory, however, every time when I ran
> "R>make.cdf.package(my.CDF file), the error message I got was "the function
> creatPackage could not be found", disregarding what platform I used to run
> R, either unix or windows version.
> -> On the other hand, I was able to run R>make.cdf.env(my.CDF file) to
> simply creat the CDF environment. However, when I proceed to further
> analysis such as those functions in "affy" library, the error message I got
> was "Error in .local(object, ...) : Information about probe locations for
> XXXXXXXX could not be found. Try downloading the XXXXXXXX package from
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html". So it appeared that
> by just creating the environment is not enough and I still need the CDF
> package.
> My questions are the follows:
> 1) what is the function called "creatPackage"? Is this function supposed to
> be built inside the "makecdfenv" package? If not, how should I check or look
> for this function?
> 2) Is there anything else I should do to, in addition to just creating the
> environment, to make the CDF environment work?
> Thanks you very much for your help!
> joan
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