Dear R helpers, I've used clValid package and use these command lines as following. one2one.stability.hk <- clValid(obj=t(prep), nClust=c(2:4), clMethods = c("hierarchical", "diana", "fanny","som","model"), validation = "stability", maxitems = 13, metric = "correlation", method = "ward", neighbSize = 10, annotation = NULL, GOcategory = "all", goTermFreq=0.05,dropEvidence=NULL,verbose=FALSE) During the process, the message The "ward" method has been renamed to "ward.D"; note new"ward.D2" keep showing unrelently. It is not the warnings and I can't manage to find a way to stop them. Would you please suggest me how to deal with the problem? Best Regards, Kaj -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] clValid_0.6-6 cluster_1.15.2 loaded via a namespace (and not attached): [1] class_7.3-10 -- Sent via the guest posting facility at bioconductor.org.

Hi Kaj, Have a look at 'suppressMessages' and 'suppressWarnings'. Best wishes Julian On 21.07.2014 07:13, Kaj Chokeshaiusaha [guest] wrote: > Dear R helpers, > > I've used clValid package and use these command lines as following. > one2one.stability.hk <- clValid(obj=t(prep), nClust=c(2:4), > clMethods = c("hierarchical", "diana", > "fanny","som","model"), > validation = "stability", > maxitems = 13, > metric = "correlation", method = "ward", > neighbSize = 10, > annotation = NULL, > GOcategory = "all", goTermFreq=0.05,dropEvidence=NULL,verbose=FALSE) > > During the process, the message > The "ward" method has been renamed to "ward.D"; note new"ward.D2" > keep showing unrelently. It is not the warnings and I can't manage to find a way to stop them. Would you please suggest me how to deal with the problem? > > Best Regards, > Kaj > > -- output of sessionInfo(): > > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] clValid_0.6-6 cluster_1.15.2 > > loaded via a namespace (and not attached): > [1] class_7.3-10 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 >