[BioC] Trouble in making the cdf package for Arabidopsis?

[Hua Liu]

Thanks for the help. I got the cdf file of the Arabidopsis ATH1 array (ATH1-121501.cdf) and tried to make the cdf package from it. I got the ath1121501cdf package by R, however, this package only contains folder data, R, man, and files DESCRIPTION, INDEX, TITLE, while the packages in the Bioconductor webpage contains a lot more folders. Below is how I did it in R. I am wondering what went wrong??

> make.cdf.env("ATH1-121501.cdf")
Reading CDF file.
Creating environment
Wait for about 228 dots......................................................................................................................................................................................................
<environment: 01983B04>

> make.cdf.package("ATH1-121501.cdf")
Reading CDF file.
Creating environment
Wait for about 228 dots............................................................................................................................................................................................................................................
[1] TRUE

> library(ath1121501cdf)
Error in testRversion(descfile) : This package has not been installed properly
 See the Note in ?library


-----Original Message-----
From: "Rafael A. Irizarry" <ririzarr@jhsph.edu>
To: Hua Liu <hliu0@uky.edu>
Date: Sun, 02 Mar 2003 09:49:02 -0500 (EST)
Subject: Re: [BioC] Bioconductor cdf package for Arabidopsis?

if you have the cdf file, you can use the package makecdfenv to make you
own. if you do bioconductor would appreciate you contribute it.


On Sat, 1 Mar 2003, Hua Liu wrote:

> I want to study the probel level data from Affymetrix Arabidopsis Genome ATH1 Array. I loaded the agcdf pachage, but the folloing R result shows that agcdf does not match this new Arabidopsis ATH1 array: 
> 
> > data<-ReadAffy("f:/doc/agl15/WS-1_ATH1.CEL")
> > data
> AffyBatch object
> size of arrays=712x712 features (3963 kb)
> Error in .local(object, ...) : Information about probe locations for ATH1-121501  could not be found.
> Try downloading the ath1121501cdf package from
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> 
> Is there a cdf package that is suitable for this array? Thanks,
> 
> Liu
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>