Question: What Are The Softwares Can Be Used For Hierarchical Clustering?
2
gravatar for Priyanka
7.7 years ago by
Priyanka30
Priyanka30 wrote:

Hi Biostars!

I have generated a matrix of numbers and wanted to do hierarchical clustering. Could anyone suggest me any tools or softwares for hierarchical clustering of the matrix (which is in csv format in a excel sheet).

Thanks

clustering • 3.0k views
ADD COMMENTlink modified 7.7 years ago by Obi Griffith18k • written 7.7 years ago by Priyanka30
4
gravatar for seidel
7.7 years ago by
seidel6.9k
United States
seidel6.9k wrote:

A really easy to use, general tool for clustering numbers is MeV (MultiExperiment Viewer), that originally came from TIGR and has been publicized by John Quackenbush for years. It's free, java-based, runs on any platform, has many tools for clustering and working with clusters, and is designed to be simple and easy to use. It's easy to install, and is the most straightforward way I know for most users (especially biologists) to cluster a table of data, and modify color themes and scaling.

ADD COMMENTlink written 7.7 years ago by seidel6.9k
3
gravatar for Obi Griffith
7.7 years ago by
Obi Griffith18k
Washington University, St Louis, USA
Obi Griffith18k wrote:

When I first starting clustering data I found this page to be helpful. It includes links to both the original and improved versions of cluster/treeview. It also links to clustering libraries for python, perl and C. The latter was useful to me when I starting having memory/runtime issues with some of the other methods (if you have very large input files). However, these days I always go to R for clustering. The 'R & Bioconductor Manual' by Thomas Girke has a nice tutorial on clustering in R that covers all manner of clustering approaches with code examples and exercises.

ADD COMMENTlink written 7.7 years ago by Obi Griffith18k
1

The benevolence of Alok Saldanha's greeting: "Hello How are you Gentlepeople!" on the TreeView page is infamous, and will never wear off. I too use and recommend R for clustering (though I assumed that @Priyanka's csv format/excel comment implied no familiarity with R). That tutorial you pointed to is really nice.

ADD REPLYlink written 7.7 years ago by seidel6.9k

Thanks @Obi... i tried using R commands but it showing a error "Error in if (n < 2) stop("must have n >= 2 objects to cluster") : argument is of length zero"

ADD REPLYlink written 7.7 years ago by Priyanka30

You have to call a distance function on your data matrix before giving it to hclust. For instance: hclust(dist(myData)). Look at the examples in the tutorial above.

ADD REPLYlink written 7.7 years ago by seidel6.9k

Thanks a lot :-) nice tutorial i must say..

ADD REPLYlink modified 7.7 years ago • written 7.7 years ago by Priyanka30
0
gravatar for Echo
7.7 years ago by
Echo40
Echo40 wrote:

The cluster and treeview will help you a lot! you can have a try!

ADD COMMENTlink written 7.7 years ago by Echo40
0
gravatar for Paulo Nuin
7.7 years ago by
Paulo Nuin3.7k
Canada
Paulo Nuin3.7k wrote:

Just use R

hclust

ADD COMMENTlink written 7.7 years ago by Paulo Nuin3.7k

i tried using R. the error its showing is "Error in if (n < 2) stop("must have n >= 2 objects to cluster") : argument is of length zero"

ADD REPLYlink written 7.7 years ago by Priyanka30

If you post your code here, someone might be able to help you...

ADD REPLYlink written 7.7 years ago by Madelaine Gogol5.1k
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