[Bioc-devel] Wiki discussion on classes for Illumina data

Sean Davis sdavis2 at mail.nih.gov
Wed Sep 5 15:07:51 CEST 2007

Mark Dunning wrote:
> Hi all,
> As you may know, there are currently multiple packages available  
> within Bioconductor for the analysis of Illumina data, all of which  
> offer different functionality and therefore users might want to use  
> multiple packages to analyse their data.
> However, each package uses a slightly different class structure to  
> read and represent the data, which could make it awkward for users to  
> translate between the packages. I'm sure you would agree that a  
> unified way of storing Illumina data, would be desirable and  
> therefore a wiki page has been created to allow users and developers  
> to discuss to the best to move forward with this.

I agree this is a good idea.  A unified parser and an
IlluminaExpressionSet makes a good deal of sense to me.  In the short
term, these could go into an IlluminaBase package and, once stable,
could potentially be moved into biobase?

I'm not sure that it is a good idea to rely on a plugin for BeadStudio,
though, to solve the parser problem.  Most users will never use it; in
many cases the users of the data will not even have access to the
software to produce it.  There is, of course, no reason not to make such
a plugin and make it available, but I think it will be difficult to get
everyone to use it before using bioconductor packages.

A little outside the discussion is the fact that Illumina can be used
for methylation, SNP, copy number (a bi-product of snps), and
potentially other uses, so when naming classes and annotation packages,
it might be worth taking this into account.


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