Hi, Is there any bioconductor packages to allow the extraction of data from the BASE microarray database (http://base.thep.lu.se/) within R. There seems to be some plugins to allow one to perform microarray analysis using R within BASE, but nothing about how to get data when within R. I know this is possible from within GeneSpring (with the appropriate plugin), so I thought there might be a way to do it from within R. Many Thanks Daniel Brewer -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research

On 7/14/06, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> wrote: > Hi, > > Is there any bioconductor packages to allow the extraction of data from > the BASE microarray database (http://base.thep.lu.se/) within R. There > seems to be some plugins to allow one to perform microarray analysis > using R within BASE, That is the aroma.Base package (http://www.braju.com/R/) and it is compatible with BASE v1.2; The upcoming BASE v2 is totally different, although they plan to be backward compatible with v1.2 plugins. > but nothing about how to get data when within R. I > know this is possible from within GeneSpring (with the appropriate > plugin), so I thought there might be a way to do it from within R. The aroma.Base package has classes to communicate data with BASE v1.2 to plugins, which is done via stdout/stdin. However, the package has *no* code for interaction with the BASE database, but you should be able to use SQL from R to access the database. BUT BUT BUT, I'm not sure if you're really supposed to do this with BASE v1.2 - you have to check with the BASE people about this. In BASE v2 there is/will be a database API, which will be implemented in Java and I guess you could setup the same API in R. Check BASE devel for more details. I have no immediate plans to implement BASE v2 in aroma.Base (because my priorities are elsewhere right now). Cheers Henrik > > Many Thanks > > > Daniel Brewer > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >