[BioC] getting closer on YEAST 2.0 annotation...

[John Zhang]

>I've gotten closer to getting a working yeast annotation package for 
>the Affymetrix YEAST 2.0 chip.  I was able to procure the proper ORF 
>ids and the probe ids, and from there I used yeastPkgBuilder within 
>AnnBuilder to create a package.  It ran for a few hours and terminated 
>with the following error:
>
>Error in readLines(con) : cannot open the connection

The code was trying to access a public data source (most likely GO based on the 
time spent) when the site was probably down.

>
> From what I can tell, it got most (if not all) of the probes processed. 
>  I tried installing the package from the shell using
>
>R CMD INSTALL YEAST2
>
>YEAST2 is the name I gave to the package.  I get the error:
>
>WARNING: invalid package 'YEAST2'
>ERROR: no packages specified

Was there a DESCRIPTION file. The build was interrupted and the package may not 
have all the required elements for a package.

>
>I know it's there, it just doesn't think the directory is a valid 
>package (dir includes R, man, data subdirectories).  I also tired 
>installing via the Mac OS X GUI, which also failed.
>
>There was also an XML file made, which seems to contain all the proper 
>annotation.  Is there any way to create an annotation package from this 
>XML file?  Why even make the XML file? (Just curious).

You can set makeXML = FALSE to turn it off.

>
>Thanks in advance,
>
>Jake Michaelson
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084