Re: [Jtreeview-users] Error message

[Alok S. <al...@ca...>]

The problem is the _A in the file name. For reasons that are not worth
going into right now, this causes Java Treeview to treat the file as  
a k-means
  clustered file instead of a hierarchical clustered file. This behavior
will hopefully go away later.

There are two solutions to this problem right now:

1) When you open the file, select "Linked" or "Classic" in the style
  pulldown of the "Open.." dialog. You may not have noticed it, but it's
there.
  Also, treeview will remember what you picked if you select it from the
  recent files list.

2) Don't use "_G" or "_A" in your file names.

     -Alok

On Nov 9, 2005, at 2:25 PM, Holweg, Cecile wrote:

> Dear Sir, Madam,
> I tried to visualize a cluster in Java Treeview and get the error  
> message copied below. I did the clustering with the Eisen cluster  
> program. I used this before with other datasets and had no problems  
> to visualize it in Java Treeview. The file I used now to cluster my  
> data is similar in format, but gives the error massage when I load  
> the file. When I do dismiss, I do get the heatmap, but the trees  
> are not there.
>
> Can you tell me what goes wrong? I tried to find it in the manual  
> but was unable to find it.
> Thank you,
> Cecile
>
>
> parsing kag
> error parsing KAG: LoadException 1: Url H:\Data\Stanford\microarray 
> \analysis files\analysis 102605\median clustering genes\cluster  
> common genes 0_1B_AR.kag could not be opened: unknown protocol: h
>
> ignoring array k-means clusters.
> loading H:\Data\Stanford\microarray\analysis files\analysis 102605 
> \median clustering genes\cluster common genes 0_1B_AR.cdt ...
>
> Finding Cdt Dimensions
> Loading Array Annotations...
> Loading Gene Annotations...
> Parsing strings into doubles...
> parsing jtv config file
>
>
>
> Cecile Holweg, PhD
> Falk CVRC
> Stanford University Medical Center
> 300 Pasteur Drive
> Stanford CA 94305-5406
> USA
> Tel: 650 725 3775
> Fax: 650 725 1599
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