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

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. HTH, Richard Park -----Original Message----- From: Caroline Johnston [mailto:johnston@biochemistry.ucl.ac.uk] Sent: Wednesday, October 22, 2003 13:40 PM To: bioconductor@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 interface. Many Thanks, Cass _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor