Sorry, I meant 'id.rep', not 'ir.rep', see below... Pierre Neuvial wrote: > Hi James, > > As for your first question, I have not done anything like this before. In our software CAPweb which includes normalisation with MANOR, we work with text files only. > > I can answer your 2nd question: it is possible. The creation of arrayCGH objects is documented (in the GLAD package, see ?arrayCGH). What you need to create an arrayCGH object is a data.frame 'arrayValues' with reporter-level (spot-level) information, and a vector 'arrayDesign' which specifies the block/spot design of the array. > > a <- list(arrayValues=arrayValues, arrayDesign=arrayDesign) > class(a) <- "arrayCGH" > > In order to perform normalisation within MANOR you should add to this object a data.frame 'cloneValues' containing annotation information for the probes. 'cloneValues' and 'spotValues' should have a common column name that will be used to merge 'arrayValues' and 'cloneValues', say "id": > > a$cloneValues <- cloneValues > a$ir.rep <- "id" a$id.rep <- "id" > > Hope this helps, > > Pierre. > > James Morris wrote: >> Hello, >> >> I would like to able to run a MANOR normalisation from data retrieved from a database, >> >> could anybody tell me if they have done anything like this before? >> >> also is it even possible to create an MANOR arrayCGH object without a file? >> >> Thanks >> >> James >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> . >> > > _______________________________________________ > 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 > > . >