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[Bioc-devel] Updated annotation data for TESTING

3 messages · Aedin Culhane, Robert Gentleman

Original
Aedin Culhane
# 
Dear Seth

I know this can be inferred from the package name. But to make it easier
to browse the packages, would it be possible to a add a few description
columns to the metadata webpage.  

For example Organism/Species, platform (Affymetrix/ABI/Agilent/MWG etc),
type (microarray/CGH etc) and perhaps the number of spots/probes. Also
perhaps a platform (ArrayExpress or GEO) accession number.  This would
make it a lot easier to browse and find a specific annotation package.  

Perhaps the simplest to implement would be to include an additional chip
name similar to the resourcerer chip names
(http://biocomp.dfci.harvard.edu/cgi-bin/magic/r1.pl).


Thanks
Aedin
Robert Gentleman
# 
Hi Aedin,
   These are all good suggestions. Do you happen to have code, or 
explicit instructions on how to obtain platform (ArrayExpress or GEO) in 
an automated fashion? It seems like it could be pretty time consuming to 
do this by hand.

   best wishes,
    Robert
Aedin wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Aedin Culhane
    

    

      
      #
    

  


  

      
Sorry Robert.

I agree. My methods are pretty "old style", I tend to sort the platform
(GPL) number on GEO, bring down the list and just text extract it (Affy
u133a is GPL96).  On AE, the tend to put in the manufactory name and
guess (u133a is A-AFFY-33).
I've copied Tanya Barrett at GEO, and Helen Parkinson at AE in on this,
as I am sure they can point out how best to do this.

Regards
Aedin

-----Original Message-----
From: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
Sent: 07 September 2005 14:52
To: Aedin
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] Updated annotation data for TESTING


Hi Aedin,
   These are all good suggestions. Do you happen to have code, or 
explicit instructions on how to obtain platform (ArrayExpress or GEO) in

an automated fashion? It seems like it could be pretty time consuming to

do this by hand.

   best wishes,
    Robert

        
Aedin wrote:

            

      
      
      
    

        
annotation package.