Hi! I am new to bioconductor: what bi-clustering algorithm is behind the function "heatmap"? Plus, is it possible to enforce that the order of timepoints remains intact? Thanks, Michaela ### "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it." -- Max Planck [[alternative HTML version deleted]]

Hi Michaela, These sorts of things are answered in the help pages. ?heatmap gives us: hclustfun: function used to compute the hierarchical clustering when 'Rowv' or 'Colv' are not dendrograms. Defaults to 'hclust'. Should take as argument a result of 'distfun' and return an object to which 'as.dendrogram' can be applied. and you can get more information about the hclust function at ?hclust. Also from ?heatmap: Note: Unless 'Rowv = NA' (or 'Colw = NA'), the original rows and columns are reordered _in any case_ to match the dendrogram, e.g., the rows by 'order.dendrogram(Rowv)' where 'Rowv' is the (possibly 'reorder()'ed) row dendrogram. So if you want a dendrogram, then no you cannot keep the original order. Otherwise you can. Best, Jim Michaela Oswald wrote: > Hi! > > I am new to bioconductor: what bi-clustering algorithm is behind the > function "heatmap"? Plus, is it possible to enforce that the order of > timepoints remains intact? > > Thanks, Michaela > > > ### > "A new scientific truth does not triumph by convincing its opponents > and making them see the light, but rather because its opponents > eventually die and a new generation grows up that is familiar with it." > > -- Max Planck > > > > > > > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

Try setting the option Colv=NA as in: heatmap(fitMvsMT0$coefficients[myGenes,], Colv=NA) and ?heatmap you may also find that heatmap.2 which you can get in the gplots library is more flexible/prettier best, yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html On Oct 29, 2008, at 14:09 , Michaela Oswald wrote: > Hi! > > I am new to bioconductor: what bi-clustering algorithm is behind the > function "heatmap"? Plus, is it possible to enforce that the order of > timepoints remains intact? > > Thanks, Michaela > > > ### > "A new scientific truth does not triumph by convincing its opponents > and making them see the light, but rather because its opponents > eventually die and a new generation grows up that is familiar with > it." > > -- Max Planck > > > > > > > > > > > [[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