On 2011-11-21 17:08, Nantel Andre wrote:
> Greetings,
> We are currently trying to integrate BASE into our lab and writing the
> necessary plug-ins to import normalized data from ImaGene. Let's just
> say that the lack of documentation has been "challenging".
> Right now we are trying to figure out how to deal with duplicate spots.
>  From the GenePix examples in the Base2 server we see cases of raw
> biosassays wtih [raw] columns defined by the unique spot coordinates as
> well as “rep‘ columns containing the duplicated GeneID classifiers. Any
> suggestions on how to do this?

What do you mean with a duplicate spots? Physically a spot is a spot and 
there can of course only be one on a given position. However there is 
nothing in BASE that prevents two or more spots from referencing the 
same gene/reporter. Then there are some platforms (for example Illumina 
BeadArrays) that doesn't have spots in the classical meaning. In this 
case one need to construct a unique "feature id" for each "spot 
equivalent" that one wants to measure. In the Illumina case, the unique 
ID is provided by the "Illumicode" column in the data files. This value 
is then mapped to gene/reporter annotations via a BGX file, and the 
importer is also calculating means, etc for all entries with the same 
"Illumicode" value. See 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina for more 
information about how the Illumina platform has been implemented.

I don't know what kind of data files that are generated by the ImaGene 
platform, so it is hard to advice on exactly how to the same thing for 


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