I have run find.hmm.states by: aCGH.hmm <- find.hmm.states(aCGH) on an aCGH object. That seems to run fine as it displays its processing of each chromosome for every sample. I follow it with hmm.merged(aCGH.hmm) <- mergeHmmStates(aCGH.hmm) as per the manual. This nomenclature looks strange so I tried the more normal aCGH.hmm.merged <- mergeHmmStates(aCGH.hmm) However both commands give the error Error in mergeHmmStates(aCGH.hmm) : compute the hmm states first using find.hmm.states What's going on? Why is it asking me to do something that I have just done? Thanks, Cian

Hi Cian, If you look closely, in the first call, you missed something and you should always operate on the same object. hmm(aCGH) <- find.hmm.states(aCGH) In your case aCGH.hmm only keeps the returned value of the function, but the original object aCGH was lost. So the error tells you mergeHmmStates can not find the $hmm slot of the object. hmm() or hmm.merged() is merely a setter for some specific slot of the aCGH object. So please follow the code exactly in the vignette unless you know what is going on behind the scene. HTH, Dan On Wed, 2013-09-18 at 12:51 +0100, Cian Murphy wrote: > I have run find.hmm.states by: > > aCGH.hmm <- find.hmm.states(aCGH) on an aCGH object. That seems to run > fine as it displays its processing of each chromosome for every sample. > I follow it with > > hmm.merged(aCGH.hmm) <- mergeHmmStates(aCGH.hmm) as per the manual. > This nomenclature looks strange so I tried the more normal > aCGH.hmm.merged <- mergeHmmStates(aCGH.hmm) > > However both commands give the error > > Error in mergeHmmStates(aCGH.hmm) : > compute the hmm states first using find.hmm.states > > > What's going on? Why is it asking me to do something that I have just done? > > Thanks, > > > Cian > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor