Hi All: I am clustering ~500 genes using hclust of R. Visualizing cluster membership in the dendrogram becomes impossible with so many genes in each cluster. with all the labels overlapping..Is there a way of printing the dendrogram on multiple pages so that I can clearly see what is in each cluster? Or is there a way of splitting the tree so that I see what is in each cluster....? Again, how would I test the significance of clustering...i mean a measure of telling how tight my clusters are, and how separated they are from each other. Thanks in advance. Karthi.

On Wed, Sep 24, 2003 at 01:20:48PM -0400, Subramanian Karthikeyan wrote: > Hi All: > > I am clustering ~500 genes using hclust of R. Visualizing cluster > membership in the dendrogram becomes impossible with so many genes in each > cluster. with all the labels overlapping..Is there a way of printing the > dendrogram on multiple pages so that I can clearly see what is in each > cluster? Or is there a way of splitting the tree so that I see what is in > each cluster....? cutree will cut the tree > > Again, how would I test the significance of clustering...i mean a measure > of telling how tight my clusters are, and how separated they are from each > other. that's harder - there are books, chapters in books and many papers on the subject - Gordon's book, Classification (which is mainly about clustering, in the sense you are using the word) has some good explanations of different methods; but there are, as I said, many others > > Thanks in advance. > > Karthi. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

HI Robert, Thanks but I am not sure how cutree works. I tried this: x = read.delim("filename.txt", row.names = 1) xdist = dist(x, method = "euclidean") xclust = hclust(xclust, method = "complete") plot(xclust) this produces the nice dendrogram of clusters cut1 = cutree(xclust, k = 2) plot(cut1) just produces a plot of (some) points in 2 D....no lines no cluster..what I really wanted to see is a section of my original dendrogram so that I can read the genes clustered together clearly. how do we achieve this? Thanks again. Best regards, Karthi. Robert Gentleman <rgentlem@jimmy.h to:="" subramanian="" karthikeyan="" <subramanian_karthikeyan@hc-sc.gc.ca=""> arvard.edu> cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] splitting clusters and cluster significance 09/24/03 02:40 PM On Wed, Sep 24, 2003 at 01:20:48PM -0400, Subramanian Karthikeyan wrote: > Hi All: > > I am clustering ~500 genes using hclust of R. Visualizing cluster > membership in the dendrogram becomes impossible with so many genes in each > cluster. with all the labels overlapping..Is there a way of printing the > dendrogram on multiple pages so that I can clearly see what is in each > cluster? Or is there a way of splitting the tree so that I see what is in > each cluster....? cutree will cut the tree > > Again, how would I test the significance of clustering...i mean a measure > of telling how tight my clusters are, and how separated they are from each > other. that's harder - there are books, chapters in books and many papers on the subject - Gordon's book, Classification (which is mainly about clustering, in the sense you are using the word) has some good explanations of different methods; but there are, as I said, many others > > Thanks in advance. > > Karthi. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+