[BioC] microarray data representation

Park, Richard Richard.Park at joslin.harvard.edu
Wed Oct 22 20:01:25 MEST 2003

Hi Cass, 
I've done something similar to what you are looking to do. My PI and I decided on our own formats as compared to exprset to make it easier for the standard biologist to use. If you are thinking of a java interface into R, you may want to look into dcom automation server. I have made a visual basic interface that communicates with S-plus/arrayanalyzer through its automation server. 

The biologists like it much more, but it has definitely been a learning process streamlining the process. We've been able to streamline it so that any new user should be able to background correct, normalize, plot, and make lists within an hr of starting it. 

Richard Park 

-----Original Message-----
From: Caroline Johnston [mailto:johnston at biochemistry.ucl.ac.uk]
Sent: Wednesday, October 22, 2003 13:40 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] microarray data representation

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 

Many Thanks,


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