[BioC] new codelink annotation packages.

[Diego Diez]

Dear BioC users,

 From now there are available annotation packages for the Codelink  
platform (GE
Healthcare). The packages can be found in the url:

http://www.bioconductor.org/packages/release/data/annotation/

and can be installed using the usual ways.

The available packages are:

h10kcod - human uniset I (~10k probes)
h20kcod - human uniset I (~20k probes)
hwgcod  - human whole genome (~50k probes)

m10kcod - mouse uniset I (~10k probes)
m20kcod - mouse uniset I (~20k probes)
mwgcod  - mouse whole genome (~35k probes)

r10kcod - rat uniset I (~10k probes)
rwgcod  - rat whole genome (~30k probes)

These packages have been built with the same repository version as  
the BioC 1.8 release, using the mapping from codelink identifiers to  
genbank available from the manufacturers web site.

Current issues:

- some probes map to:
     * CODELINK_UNIQUE
     * COMPUGEN_UNIQUE
     * INCYTE_UNIQUE
  with no other information except for some where Unigene identifier  
were used. I have set all those probes to NA.

- some probes map to CONTROL probe identifiers (from codelink). I  
have set those to NA.

- some probes map to multiple Genbank identifiers. I have used all  
available identifiers.

- some probes are in duplicate in the gene list, because they are  
also CONTROL probes. I have set it to the available Genbank identifier.

- r10kcod have some old codelink identifiers (i.e. not using GExxxxx  
system) this is not and issue except if they decide to change the  
identifiers later.


I would like to thank Nianhua Li and Ting-Yuan Liu for his efforts  
helping me in this task and also for the availability of the windows  
binary packages. MacOSX binary packages are not yet available but it  
will be soon thanks to Simon Urbanek. I would like also to thank all  
the people that make the Bioconductor project possible.


Best regards,

Diego Diez.