Hi all,
Our site will likely wish to store Illumina array data in BASE 2 in
the near future. Sifting through the mailing list archive, this seems
indeed possible (based on the post below, from july '06).
My question is has anyone implemented this already (Reha Y.?) and is
willing to share the specifications and/or will this find its way
into BASE 2 proper some day?
regards,
/Emil
________________________________
Emil Lundberg / Sysadm
Linnaeus Centre for Bioinformatics
Uppsala University
Reha Yildirimman wrote:
> Hello,
>
> using Base2 we are trying to implement the Illumina Chip design.
In order
> to use the raw data files describing coordinates and intensities
of probes
> there is a need to define a new raw data type besides the given ones
> (affymetrix,agilent,spotfinder,...).
>
> Is this already implemented, is there a way around the "data
type" problem
> or am I looking at the wrong spot in base2 ?
Yes, you can add raw data types to Base2. You have to find and modify
the file 'raw-data-types.xml'. It should be located in the
<basedir>/www/WEB-INF/classes directory.
Add a tag <raw-data-type> for the Illumina Chip for example:
<raw-data-type
id="illumina"
channels="2"
name="Illumina"
table="RawDataIllumina"
>
Then add as many <property> tags as you need. The last step is to run
the <basedir>/bin/updatedb.sh script to create the new table.
/Nicklas
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