Hello everybody, I am using the hclust() function in R. I have a 2000*12 matrix of expression data. I have created a distance matrix with dist() using Euclidean method. Then in hclust I have used complete linkage method. Now when I am trying to plot the dendogram with pclust method I cannot see the details of the tree. The gene names and the lower parts of the dendogram are not visible Is there any method by which I can see only selected parts of the dendogram.....or Zoom in or out.... I have used the follwing command for pclust: plclust(H2000, unit = FALSE, level = FALSE, hmin = 0, + square = TRUE, labels =names2000 , plot. = TRUE, + axes = TRUE, frame.plot = FALSE, ann = TRUE, + main = "", sub = NULL, xlab = NULL, ylab = "Height") I am attaching a snapshot of the dendogram that I am getting. Please help ASAP. Thanks in advance, Madhurima.

Hi dendrograms were designed for and intially applied to significantly smaller problems then 2,000 objects. I cannot imaging how to dispaaly a tree with that many terminal nodes in such a way to be able to read the labels. You might try using 'cutree' into a dozen or so subtrees and plot each subtree individually. You might also try using kmeans to partition the data with that large a sample. Bill --- Biostatistics Consulting Center http://ilya.wustl.edu/~shannon/bcc_announcement.pdf "Statistics is not a discipline like physics, chemistry or biology where we study a subject to solve problems in the same subject. We study statistics with the main aim of solving problems in other disciplines." CR Rao William D. Shannon, Ph.D. Associate Professor of Biostatistics in Medicine Division of General Medical Sciences and Biostatistics Washington University School of Medicine Campus Box 8005, 660 S. Euclid St. Louis, MO 63110 Phone: 314-454-8356 Fax: 314-454-5113 e-mail: wshannon at wustl.edu web page: http://ilya.wustl.edu/~shannon

Dear, For a convenient tree browssing, you can use an external software: freeview or treeview (http://magix.fri.uni-lj.si/freeview). Package ctc is usefull to export R hclust object to freeview/treeview file format. Regards, Antoine Lucas. Le Tue, 08 Nov 2005 18:25:15 +0530 madhurima bhattacharjee <madhurima_b at="" persistent.co.in=""> a ?crit: > Hello everybody, > > I am using the hclust() function in R. > I have a 2000*12 matrix of expression data. > I have created a distance matrix with dist() using Euclidean method. > Then in hclust I have used complete linkage method. > Now when I am trying to plot the dendogram with pclust method I cannot > see the details of the tree. > The gene names and the lower parts of the dendogram are not visible > Is there any method by which I can see only selected parts of the > dendogram.....or Zoom in or out.... > I have used the follwing command for pclust: > plclust(H2000, unit = FALSE, level = FALSE, hmin = 0, > + square = TRUE, labels =names2000 , plot. = TRUE, > + axes = TRUE, frame.plot = FALSE, ann = TRUE, > + main = "", sub = NULL, xlab = NULL, ylab = "Height") > > I am attaching a snapshot of the dendogram that I am getting. > Please help ASAP. > > Thanks in advance, > Madhurima. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Antoine Lucas Centre de g?n?tique Mol?culaire, CNRS 91198 Gif sur Yvette Cedex Tel: (33)1 69 82 38 89 Fax: (33)1 69 82 38 77