Java Treeview With Kmeans

Question

[Varun Gupta]

Hi Everyone

I am using Java TreeView software for generating some heatmaps. I used Cluster software on my list of 22000 genes and generated .cdt files which are input for Java Treeview

I run this command to open up the interface of treeview software

java -jar -Xmx500m /apps1/treeview/1.1.6r2/TreeView.jar

File ---> Open -->Selecting appropriate .cdt file ----> style as kmeans

Now here's the problem. When i do style as kmeans a heat map is generated. I change the pixels and all so as to view it better and try to save the image by going to Export---> Save Tree Image

But nothing happens. When i use the style as linked i can save the images.

I am not sure but is it because i have around 22000 genes and around 50 columns which is not letting me save the image of the heatmap on the kmeans style.

Hope to find solution here.

Regards

V

Answer 1

[kanwarjag]

http://www.broadinstitute.org/cancer/software/genepattern/modules?utf8=%E2%9C%93&taskType=Clustering

Take matrix of clustering and plot in R or use cluster image viewer. I thought it has worked for me.

[Josh Herr]

Please add this to the answer you posted above. It is not another answer to the question, but a clarification on your previous post. Please also review the "About" tab for more information on how to best ask questions and provide answer to the community. Thanks for your input!

Answer 2

[kanwarjag]

though not a direct answer to your question, But I can point out use Gene pattern on Broad it will do the same job. There are some issues I have encountered with 64 bit machines. But I am not sure if that is the same issue you are facing. But Broad site will keep you going.

[Varun Gupta]

Hi Does it take .cdt as input. I haven't used it that's y i am asking this.

[kanwarjag]

Yes it will allow you to add custom cdt files as well as you can upload your data in .GCT format it will generate adt, cdt files which can be used into to generate image. You have to browse the site there are tutorials. best

[Josh Herr]

In the future it would be helpful if you gave some information about what you are referring to: I looked for "Gene pattern on Borad" and did not find anything.

You can link to relevant sites, programs, and scripts here and that would be the best way to both help the person asking the question as well as the community as a whole.