[BioC] microarray data representation

[Caroline Johnston]

Hi List,	

We were thinking about developing a java interface to some of the
Bioconductor tools as the biologists we're working with aren't too keen on 
doing command line stuff.

They're using spotted and affy chips and I would really like a single
interface for both. Is there any consensus within Bioconductor about
object representation of microarray experimental data?  I've looked at the
AffyBatch and ExprSet classes in affy, but I don't know about cDNA arrays
(should I be looking at limma?). Are there other Bioconductor tools that
use different classes, or is, say ExprSet, a standard representation?  
Are there any generic methods defined for doing certain steps of the
analysis, regardless of platform (I've not done any spotted analysis yet,
but I'm assuming there are quite a few similar steps to affy analysis,
even if the implementation is different)?

Also, if anyone who is using Bioconductor for microarray analysis has the 
time to email a list of their favourite tools, it would be really useful 
when trying to decide what to make available in our first attempt at an 
interface. 

Many Thanks,

Cass