Hallo BioC list, I am analysing 38 two color arrays for a time course experiment with dye swap (5 time points). I have used maanova for normalisation and macluster() for clustering (see code below). Now, I am wondering how to extract the log ratios (R/G) for each gene for each time point. The consensus() function plots these values, and I would like to know how to get them. Thanks a lot, Heike ######################################################### maanova.raw <- read.madata("maanovafile.txt", designfile="designfile.txt", metarow=1, metacol=2, col=3, row=4, probeid=5,intensity=7, arrayType='twoColor', log.trans=T, spotflag=T) my.data<-transform(maanova.raw,method="rlowess") fit.fix<-fitmaanova(my.data,formula=~Dye+Array+Sample) cluster.kmean<-macluster(fit.fix,term="Sample", idx.gene=idx.fix$idx.all, what="gene",method="kmean", kmean.ngroups=8,n.perm=100) consensus(cluster.kmean,0.8) > sessionInfo() R version 2.7.0 (2008-04-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tcltk tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] hgu133a.db_2.2.0 maanova_1.8.1 GOstats_2.6.0 [4] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 [7] RBGL_1.16.0 graph_1.18.1 annotate_1.18.0 [10] xtable_1.5-1 org.Hs.eg.db_2.2.0 goProfiles_1.2.0 [13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 [16] DBI_0.2-4 marray_1.12.0 tkWidgets_1.14.0 [19] DynDoc_1.14.0 widgetTools_1.12.0 gplots_2.3.2 [22] gdata_2.2.0 gtools_2.3.0 DNAcopy_1.10.0 [25] biomaRt_1.10.0 XML_1.9-0 RCurl_0.8-0 [28] limma_2.12.0 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.10 -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312

Hello again, I have found the answer. The log ratios can be extracted using con.kmean<-consensus(cluster.kmean,thres,draw=FALSE) con.kmean$data.draw Best, Heike On Friday 22 August 2008 18:29, Heike Pospisil wrote: > Hello BioC list, > > I am analysing 38 two color arrays for a time course experiment with dye > swap (5 time points). I have used maanova for normalisation and macluster() > for clustering (see code below). > > Now, I am wondering how to extract the log ratios (R/G) for each gene for > each time point. The consensus() function plots these values, and I would > like to know how to get them. > > Thanks a lot, > Heike > > > ######################################################### > maanova.raw <- read.madata("maanovafile.txt", > designfile="designfile.txt", > metarow=1, metacol=2, col=3, row=4, > probeid=5,intensity=7, > arrayType='twoColor', > log.trans=T, spotflag=T) > > my.data<-transform(maanova.raw,method="rlowess") > > fit.fix<-fitmaanova(my.data,formula=~Dye+Array+Sample) > > cluster.kmean<-macluster(fit.fix,term="Sample", > idx.gene=idx.fix$idx.all, > what="gene",method="kmean", > kmean.ngroups=8,n.perm=100) > > consensus(cluster.kmean,0.8) > > > sessionInfo() > > R version 2.7.0 (2008-04-22) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF- >8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME= C;LC_AD >DRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tcltk tools stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] hgu133a.db_2.2.0 maanova_1.8.1 GOstats_2.6.0 > [4] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 > [7] RBGL_1.16.0 graph_1.18.1 annotate_1.18.0 > [10] xtable_1.5-1 org.Hs.eg.db_2.2.0 goProfiles_1.2.0 > [13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 > [16] DBI_0.2-4 marray_1.12.0 tkWidgets_1.14.0 > [19] DynDoc_1.14.0 widgetTools_1.12.0 gplots_2.3.2 > [22] gdata_2.2.0 gtools_2.3.0 DNAcopy_1.10.0 > [25] biomaRt_1.10.0 XML_1.9-0 RCurl_0.8-0 > [28] limma_2.12.0 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312