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

[Jacob Michaelson]

On Feb 15, 2005, at 6:52 AM, John Zhang wrote:

>
>> 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.

The following files were created:
YEAST2ALIAS.rda
YEAST2CHR.rda
YEAST2CHRLOC.rda
YEAST2DESCRIPTION.rda
YEAST2GENENAME.rda
YEAST2GO.rda
YEAST2ORF.rda
YEAST2PMID.rda
YEAST2PMID2PROBE.rda

>
>>
>> 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.

I know I can turn it off -- I just wanted to know what the purpose 
would be (within BioC) of making an XML version.

>
>>
>> Thanks in advance,
>>
>> Jake Michaelson
>>
>> _______________________________________________
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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>

Jake Michaelson

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