Hi All Not sure if this a bioconductor question or general R mailing list so apologies if this has gone to the wrong one................. When plotting dendrograms created by hclust you can "identify" clusters by clicking on the graphics and returning a list of what is contained in each cluster. However I'd like to be able to "zoom in" on specific clusters and plot them, is this possible at all ? Also I have a microarray experiment where I'd like to be able to plot A gene tree against a condition tree using the heatmap function. for genes according to treatments and viceversa I.e Treatments being DIF1, DIF2, DIF3 genes being 324c_F, 634_F etc. 393 genes x 3 treatments name DIF1 DIF2 DIF3 324c_F 4.16E-01 2.65E-01 0.298602679 634_F 8.95E-01 6.67E-01 0.337895962 504c_F 4.54E-01 5.94E-01 1.185792741 1302_F -6.43E-01 -5.39E-01 0.073152009 233c_F 4.20E-01 4.27E-01 0.261216119 1274_F -5.00E-01 -3.53E-01 -0.161567509 1314_F 1.59E+00 1.08E+00 0.403198377 1791c_F 9.08E-01 4.11E-01 0.461046812 594c_F 6.43E-01 3.93E-01 -0.142807556 854c_F -5.59E-01 -9.70E-01 -0.766361402 viseversa. 3 treatment x 393 genes name 324c_F 634_F 504c_F 1302_F.......... DIF1 4.16E-01 8.95E-01 4.54E-01 -6.43E-01...... DIF2 2.65E-01 6.67E-01 5.94E-01 -5.39E-01...... DIF3 0.298602679 0.337895962 1.185792741 0.073152009.... etc............. And would like to be able to plot one against the other. I've used as.dendrogram to create dendrograms from the output of hclust for each of the data sets mentioned above but.......... I'm having problems with the rest of the functions Could someone advise me as to which numeric matrix I should be using specified as X in the example: heatmap(x, dendrogram1, dendrogram2 etc) I.e. is X coming from the results of dist, hclust or the original data ? If so do you then need to covert it into a numeric matrix ? I've thus far tried the data.matrix function on the output from all of the above only to get: `x' must be a numeric matrix heatmap(DIF123distmatrix, hclustfun=hclust) This command works nicely but obviously plots the same thing on both axes. I've tried something along the lines of: heatmap(DIF123datamat, DIF123clustFLIPasdendro, DIF123clustHCmcquittyasdendro, hclustfun=hclust) but this returns row dendrogram ordering gave index of wrong length which has come from the viseversa example above. thanks for any help and guidance Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919