jtreeview-users — List for users to post to for help. The project administrator will read it.

[Jtreeview-users] Windows 7

[Richard F. <fri...@ca...>]

Dear Jtreeview Users.

	Has anyone had success in using Jtreeview with Windows 7.
A member of our IT staff had just tried it without success.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
fri...@ca...
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
George Scithers

Re: [Jtreeview-users] help

[Alok S. <alo...@gm...>]

Dear Mara,

As far as I know there isn't a particularly easy way. CEL and PCL
formats are both simple text formats, and In the past I have written
my own perl scripts to translate. The two other things I have heard
are

1) Try loading your CEL files in dChip or MeV, and see if they will
export to PCL. MeV has a bunch of cluster/JTV functionality built in.
2) Rearrange the files yourself in Excel. You should be able to get
the numbers keyed to gene names using the export functions in GCOS.

Maybe someone else on the list will get back to you with something easier!

On Wed, Jul 7, 2010 at 3:23 PM,  <mh...@bu...> wrote:
> Hello, I am trying to use Java Treeview with Cluster 3. I am having
> trouble getting started. The files I have are .CEL not .CDT or .PCL.
> Please help, Thanks, Mara
>
>
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[Jtreeview-users] (no subject)

[<mh...@bu...>]

Hello, I am trying to use Java Treeview with Cluster 3. I am having 
trouble getting
started. The files I have are .CEL not .CDT or .PCL. Please help, Thanks, Mara

[Jtreeview-users] help

[<mh...@bu...>]

Hello, I am trying to use Java Treeview with Cluster 3. I am having 
trouble getting started. The files I have are .CEL not .CDT or .PCL. 
Please help, Thanks, Mara

Re: [Jtreeview-users] How to load a .jtv url settings file into TreeViewApplet?

[Alok S. <alo...@gm...>]

Dear Anna,

I'm not sure I fully understand, but there is an "index" attribute that you
can set on the "UrlExtractor" and "ArrayUrlExtractor" tags that will specify
which header column, or in the case of arrays row to use. For example,

<ArrayUrlExtractor index="0" urlTemplate='$url2' isEnabled='1'/>

Should tell it to use the "AID" row instead of the "GID" row. Sorry about
the delay.

Alok

On Thu, Mar 18, 2010 at 2:06 PM, Anna Ratner <i_a...@ya...> wrote:

> Hi Alok,
>
> Changing my jtv file to what you suggested i.e.:
>
> <DocumentConfig>
> <UrlExtractor urlTemplate='$url1' isEnabled='1'/>
> <ArrayUrlExtractor urlTemplate='$url2' isEnabled='1'/>
> </DocumentConfig>
>
> instead of the previous:
>
> <ProgramConfig>
> <GeneUrlPresets>
>   <Preset name='Gene' template='$url1' header='*' enabled='true'/>
> </GeneUrlPresets>
> <ArrayUrlPresets>
>   <Preset name='Sample' template='$url2' header='*' enabled='true'/>
> </ArrayUrlPresets>
> </ProgramConfig>
>
> works and my .jtv file loads the url settings. The only problem now is that
> it inserts the "AID" values into the HEADER field instead of "GID" for the
> ArrayUrl template, so I still have to manually change the selection in the
> drop-down for url settings -> array. How do I specify which values to use
> here in my .jtv file.
>
> Thank you,
> Anna
>
>  ------------------------------
> *From:* Alok Saldanha <alo...@gm...>
> *To:* Anna Ratner <i_a...@ya...>
> *Cc:* jtr...@li...
> *Sent:* Thu, March 18, 2010 5:57:49 AM
>
> *Subject:* Re: [Jtreeview-users] How to load a .jtv url settings file into
> TreeViewApplet?
>
> Dear Anna,
>
> Most likely the jtv file is being recognized, you can be sure of it by
> changing your color (Settings->Pixel Settings, although I just noticed the
> Color label is misaligned). There seems to be something funky going on with
> the URL Settings, namely they don't seem to be actually written to disk. I
> won't have time to look into this further until the weekend, alas Java
> Treeview is on the backburner for the time being, warts and all. For now the
> best workaround is to close java treeview and manually open the .jtv file
> in  a text editor. You need to add "urlTemplate" and "isEnabled" attributes
> to the UrlExtractor tag which should be a child of DocumentConfig, which is
> the root tag of the document. Here is an example to link to google:
>
> <UrlExtractor urlTemplate="http://www.google.com/search?q=HEADER"
> isEnabled="1" />
>
> If this doesn't help send me a link to the site with a non-working applet
> and I'll take a look.
>
> Regards,
> Alok
>
> On Wed, Mar 17, 2010 at 9:58 PM, Anna Ratner <i_a...@ya...> wrote:
>
>>  Hi,
>> I am using the Jave TreeViewApplet on a web page (thank you for this
>> software!) and the problem that I am running into is that it doesn't want to
>> take my .jtv file for url settings. I found a previous issue in the archive
>> where someone was having a similar problem, but that was eventually fixed
>> according to the emails. I write the .jtv file into the same directory as
>> the .cdt, .atr, and .gtr files.
>>
>>       <APPLET
>> code="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>>               archive="$archive"
>>               width='250' height='50'>
>>         <PARAM name="cdtFile" value="$tmp_url/cluster$$.cdt">
>>         <PARAM name="cdtName" value="with Java TreeView">
>>         <PARAM name="styleName" value="linked">
>>         <PARAM name="plugins"
>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory">
>>       </APPLET>
>>
>> Also, where can I find the documentation for how to specify url settings
>> for applets?
>> Any help would be appreciated.
>> Thank you very much,
>> Anna
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
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>> See why Intel Parallel Studio got high marks during beta.
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>> _______________________________________________
>> Jtreeview-users mailing list
>> Jtr...@li...
>> https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>>
>>
>
>

Re: [Jtreeview-users] Uninstalling TreeView

[Alok S. <alo...@gm...>]

Dear Omer,

There is no uninstaller. I recommend that you use a right-click to delete
the item from the program menu, and then delete the folder in C:\Program
Files\Stanford University\Java TreeView

2010/3/13 Ömer AN <bo...@gm...>

>  Hey,
>
> How can I uninstall Java Tree View from my computer? I installed it togeter
> with Cluster 3.0 and now i removed Cluster 3.0 but can't do for Tree View.
> It is not located in Add/Remove Programs section. Can you explain how to do?
>
> My OS is Windows XP.
>
> Thanks in advance...
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
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> _______________________________________________
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>
>

Re: [Jtreeview-users] How to load a .jtv url settings file into TreeViewApplet?

[Alok S. <alo...@gm...>]

Dear Anna,

Most likely the jtv file is being recognized, you can be sure of it by
changing your color (Settings->Pixel Settings, although I just noticed the
Color label is misaligned). There seems to be something funky going on with
the URL Settings, namely they don't seem to be actually written to disk. I
won't have time to look into this further until the weekend, alas Java
Treeview is on the backburner for the time being, warts and all. For now the
best workaround is to close java treeview and manually open the .jtv file
in  a text editor. You need to add "urlTemplate" and "isEnabled" attributes
to the UrlExtractor tag which should be a child of DocumentConfig, which is
the root tag of the document. Here is an example to link to google:

<UrlExtractor urlTemplate="http://www.google.com/search?q=HEADER"
isEnabled="1" />

If this doesn't help send me a link to the site with a non-working applet
and I'll take a look.

Regards,
Alok

On Wed, Mar 17, 2010 at 9:58 PM, Anna Ratner <i_a...@ya...> wrote:

> Hi,
> I am using the Jave TreeViewApplet on a web page (thank you for this
> software!) and the problem that I am running into is that it doesn't want to
> take my .jtv file for url settings. I found a previous issue in the archive
> where someone was having a similar problem, but that was eventually fixed
> according to the emails. I write the .jtv file into the same directory as
> the .cdt, .atr, and .gtr files.
>
>       <APPLET
> code="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>               archive="$archive"
>               width='250' height='50'>
>         <PARAM name="cdtFile" value="$tmp_url/cluster$$.cdt">
>         <PARAM name="cdtName" value="with Java TreeView">
>         <PARAM name="styleName" value="linked">
>         <PARAM name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory">
>       </APPLET>
>
> Also, where can I find the documentation for how to specify url settings
> for applets?
> Any help would be appreciated.
> Thank you very much,
> Anna
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>
>

[Jtreeview-users] How to load a .jtv url settings file into TreeViewApplet?

[Anna R. <i_a...@ya...>]

Hi,
I am using the Jave TreeViewApplet on a web page (thank you for this software!) and the problem that I am running into is that it doesn't want to take my .jtv file for url settings. I found a previous issue in the archive where someone was having a similar problem, but that was eventually fixed according to the emails. I write the .jtv file into the same directory as the .cdt, .atr, and .gtr files. 

      <APPLET code="edu/stanford/genetics/treeview/applet/ButtonApplet.class" 
              archive="$archive" 
              width='250' height='50'> 
        <PARAM name="cdtFile" value="$tmp_url/cluster$$.cdt"> 
        <PARAM name="cdtName" value="with Java TreeView"> 
        <PARAM name="styleName" value="linked"> 
        <PARAM name="plugins" value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory">
      </APPLET> 

Also, where can I find the documentation for how to specify url settings for applets? 
Any help would be appreciated. 
Thank you very much,
Anna


      

[Jtreeview-users] Uninstalling TreeView

[Ömer AN <bo...@gm...>]

Hey,

How can I uninstall Java Tree View from my computer? I installed it togeter with Cluster 3.0 and now i removed Cluster 3.0 but can't do for Tree View. It is not located in Add/Remove Programs section. Can you explain how to do?

My OS is Windows XP.

Thanks in advance...

Re: [Jtreeview-users] Clustering probem

[Alok S. <alo...@gm...>]

Dear Wendy,

This can sometimes happen if the values in your data file are outside of the
expected range. You can test this by selecting a few rows on the left side
of the screen and letting your mouse linger over the rows on the right hand
of the screen (i.e. the zoomed in rows). If the values displayed are larger
than 3, the you may need to adjust the contrast settings. To do this, goto
Settings->Pixel Settings, and either use the slider or edit the number in
the Contrast box.

If this doesn't help, you can also send me a zip file containing the cdt and
gtr and I'll have a look.

-Alok


On Sat, Jan 30, 2010 at 7:29 AM, Wendy Qiao <wen...@ut...> wrote:

>  Dear there,
>
>
>
> When I try to cluster, the map is completely red. I think there is some
> problem with the clustering algorithms that I used. I tried the most of the
>  Adjust Data-Cluster combinations in Cluster3.0, but no one works. What may
> the possible reason?
>
>
>
> Thank you,
>
> Wendy
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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>
>

[Jtreeview-users] Fwd: Clustering probem

[Alok S. <alo...@gm...>]

Hi Wendy,

it looks like your data is not ratio data, but either count or intensity
data. I got good results by logscaling with a center of 6 (this means a
starting value x is mapped to y = log2(x / 6), i.e. a value of 6 is mapped
to zero, and other values are turned into fold changes relative to 6. To do
this, just open Settings->Pixel Settings, got the "LogScale" section below
the contrast section, check "Log (base 2)" , and enter 6 as the center.

If you clustered the samples, you should have an atr file which will provide
an array tree. I strongly recommend you cluster the genes as well, as that
will make it much easier to interpret the output.


On Sun, Jan 31, 2010 at 7:41 AM, Wendy Qiao <wen...@ut...> wrote:

>  Hi Alok,
>
>
>
> Thank you for your reply. I think my values are too large. There are some
> dots appearing after I increase the contrast value to the max (5), but I
> still can’t see the map. Is there a way to navigate this?
>
>
>
> My cdt file is attach. I do not have a gtr file as I only clustered the
> samples. Would that be one of the reason as well?
>
>
>
> Thank you .
>
> Wendy
>
>
>
> *From:* Alok Saldanha [mailto:alo...@gm...]
> *Sent:* January-31-10 7:22 AM
> *To:* Wendy Qiao
> *Cc:* jtr...@li...
> *Subject:* Re: [Jtreeview-users] Clustering probem
>
>
>
> Dear Wendy,
>
> This can sometimes happen if the values in your data file are outside of
> the expected range. You can test this by selecting a few rows on the left
> side of the screen and letting your mouse linger over the rows on the right
> hand of the screen (i.e. the zoomed in rows). If the values displayed are
> larger than 3, the you may need to adjust the contrast settings. To do this,
> goto  Settings->Pixel Settings, and either use the slider or edit the number
> in the Contrast box.
>
> If this doesn't help, you can also send me a zip file containing the cdt
> and gtr and I'll have a look.
>
> -Alok
>
>  On Sat, Jan 30, 2010 at 7:29 AM, Wendy Qiao <wen...@ut...>
> wrote:
>
> Dear there,
>
>
>
> When I try to cluster, the map is completely red. I think there is some
> problem with the clustering algorithms that I used. I tried the most of the
>  Adjust Data-Cluster combinations in Cluster3.0, but no one works. What may
> the possible reason?
>
>
>
> Thank you,
>
> Wendy
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
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> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>
>
>

[Jtreeview-users] Clustering probem

[Wendy Q. <wen...@ut...>]

Dear there,

 

When I try to cluster, the map is completely red. I think there is some
problem with the clustering algorithms that I used. I tried the most of the
Adjust Data-Cluster combinations in Cluster3.0, but no one works. What may
the possible reason?

 

Thank you,

Wendy 

 

 

Re: [Jtreeview-users] saving an image

[Alok S. <alo...@gm...>]

Hi Meghan,

There are basically three options

1) Try Export->Export to Postscript, which will get you a vector
graphics file that should look decent when printed.
2) You can try Export->Export to Image to get a rastered image in
either png, ppm or gif format.
3) If all else fails, take a screenshot of what you need at close to
the right resolution.

For options 1 and 2, I found I had to check the preview checkbox and
resize the dialog to get the preview to show.

Hope this helps,
Alok


On Sun, Oct 4, 2009 at 5:06 PM, meghan wyse <mm...@gm...> wrote:
> How can i save an image of the dendograph to import into a word document?
> Thank you
>
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[Jtreeview-users] saving an image

[meghan w. <mm...@gm...>]

How can i save an image of the dendograph to import into a word document?
Thank you

[Jtreeview-users] Export to Image

[wormbuff <wor...@gm...>]

I am trying to standardize the Karyoscope images that I exported from  
Java TreeView.  However, I am having difficulty understanding how  
image dimensions are determined with "Export to Image".  It appears  
that if I resize the main window by dragging the lower right corner,  
the exported image dimensions are adjusted.  The dimensions, however,  
do not match up with the "Size Width" and "Height" reported in the  
upper left frame of the main window.  Furthermore, if I attempt to  
adjust the image dimensions either in the width/height boxes in the  
main window or the window that pops up after clicking on "Export to  
Image", neither have an effect on the final exported image.  Any  
insight would be greatly appreciated.

This is in reference to Java TreeView v1.1.3 under J2RE 1.5.0_19- 
b02-306 on Mac OS X 10.4.11.

Re: [Jtreeview-users] TreeView Difficulties

[Alok S. <alo...@gm...>]

I am not sure exactly what is causing your problem. It would help if  
you could email me a stack trace (i.e. run jtv from the command line,  
when it exits it should print out something to the terminal).  Which  
version of Java are you using? I recommend downloading and installing
the version from Sun:

http://java.sun.com/javase/downloads/index.jsp

You can test what version of java you have by running

java -version

I put some effort into making it work with gcj, but java runtimes  
change quick.

	-Alok

On Oct 27, 2008, at 12:57 PM, wp...@CL... wrote:

> To Whom It May Concern:
>
>    I have just downloaded/installed the software on Linux and when  
> I run
> the application and register I always get the following error:
>
> "Could not open URL:
> http://lists.sourceforge.net/lists/listinfo/jtreeview-announce"
>
> And then the program, "disappears" into the background.  What  
> gives?   Am
> I doing something wrong?  Also, whenever I click on the other two  
> buttons
> (Register Later or Do Not Register) the program terminates.
>
> Regards,
>
> William P. Taylor II
>
> ---------------------------------------------------------------------- 
> ---
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
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> Build the coolest Linux based applications with Moblin SDK & win  
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[Jtreeview-users] TreeView Difficulties

[<wp...@CL...>]

To Whom It May Concern:

   I have just downloaded/installed the software on Linux and when I run
the application and register I always get the following error:

"Could not open URL:
http://lists.sourceforge.net/lists/listinfo/jtreeview-announce"

And then the program, "disappears" into the background.  What gives?   Am
I doing something wrong?  Also, whenever I click on the other two buttons
(Register Later or Do Not Register) the program terminates.

Regards,

William P. Taylor II

Re: [Jtreeview-users] dendrogram with treeview

[Alok S. <alo...@gm...>]

Dear fine,

You don't actually need Java Treeview, you need Cluster 3.0 from

http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm

clustering will create a file with a ".gtr" extension that has columns
corresponding to Node, Left child, Right Child and height. You will need to
parse this to create the tree that you want.

I am not aware of a good tool that will do clustering in a web browser if
that is what you want, although it would certainly be possible to port from
cluster 3.0 (which is open source).

Good luck,
Alok

On Mon, May 12, 2008 at 5:36 PM, fine cur <fi...@ya...> wrote:

> Hi, I am trying to use Treeview to generate dendrogram. I have my own
> "draw" function written alreay in Adobe Flash. So I do not need a java
> JPanel or other GUI program. I just need to use TreeView to compute the
> clusters from original data and output a descriptive result something like
> the file bellow. Could anyone tell me how to do it?
>
> --[dendrogram w/ 2 branches and 20 members at h = 10.1]
>   |--[dendrogram w/ 2 branches and 5 members at h = 3.69]
>   |  |--leaf "17"
>   |  `--[dendrogram w/ 2 branches and 4 members at h = 2.13]
>   |     |--leaf "9"
>   |     `--[dendrogram w/ 2 branches and 3 members at h = 0.352]
>   |        |--leaf "20"
>   |        `--[dendrogram w/ 2 branches and 2 members at h = 0.143]
>   |           |--leaf "18"
>   |           `--leaf "19"
>   `--[dendrogram w/ 2 branches and 15 members at h = 6.16]
>      |--leaf "6"
>      `--[dendrogram w/ 2 branches and 14 members at h = 3.05]
>         |--[dendrogram w/ 2 branches and 7 members at h = 0.82]
>         |  |--leaf "14"
>         |  `--[dendrogram w/ 2 branches and 6 members at h = 0.356]
>         |     |--[dendrogram w/ 2 branches and 3 members at h = 0.128]
>         |     |  |--leaf "15"
>         |     |  `--[dendrogram w/ 2 branches and 2 members at h = 0.110]
>         |     |     |--leaf "11"
>         |     |     `--leaf "12"
>         |     `--[dendrogram w/ 2 branches and 3 members at h = 0.217]
>         |        |--leaf "13"
>         |        `--[dendrogram w/ 2 branches and 2 members at h = 0.117]
>         |           |--leaf "10"
>         |           `--leaf "16"
>         `--[dendrogram w/ 2 branches and 7 members at h = 1.7]
>            |--[dendrogram w/ 2 branches and 5 members at h = 0.539]
>            |  |--leaf "7"
>            |  `--[dendrogram w/ 2 branches and 4 members at h = 0.223]
>            |     |--leaf "8"
>            |     `--[dendrogram w/ 2 branches and 3 members at h = 0.183]
>            |        |--leaf "4"
>            |        `--[dendrogram w/ 2 branches and 2 members at h =
> 0.107]
>            |           |--leaf "2"
>            |           `--leaf "3"
>            `--[dendrogram w/ 2 branches and 2 members at h = 0.698]
>               |--leaf "1"
>               `--leaf "5"
>
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>
>

[Jtreeview-users] dendrogram with treeview

[fine c. <fi...@ya...>]

  Hi, I am trying to use Treeview to generate dendrogram. I have my own "draw" function written alreay in Adobe Flash. So I do not need a java JPanel or other GUI program. I just need to use TreeView to compute the clusters from original data and output a descriptive result something like the file bellow. Could anyone tell me how to do it?
   
  --[dendrogram w/ 2 branches and 20 members at h = 10.1]
  |--[dendrogram w/ 2 branches and 5 members at h = 3.69]
  |  |--leaf "17" 
  |  `--[dendrogram w/ 2 branches and 4 members at h = 2.13]
  |     |--leaf "9" 
  |     `--[dendrogram w/ 2 branches and 3 members at h = 0.352]
  |        |--leaf "20" 
  |        `--[dendrogram w/ 2 branches and 2 members at h = 0.143]
  |           |--leaf "18" 
  |           `--leaf "19" 
  `--[dendrogram w/ 2 branches and 15 members at h = 6.16]
     |--leaf "6" 
     `--[dendrogram w/ 2 branches and 14 members at h = 3.05]
        |--[dendrogram w/ 2 branches and 7 members at h = 0.82]
        |  |--leaf "14" 
        |  `--[dendrogram w/ 2 branches and 6 members at h = 0.356]
        |     |--[dendrogram w/ 2 branches and 3 members at h = 0.128]
        |     |  |--leaf "15" 
        |     |  `--[dendrogram w/ 2 branches and 2 members at h = 0.110]
        |     |     |--leaf "11" 
        |     |     `--leaf "12" 
        |     `--[dendrogram w/ 2 branches and 3 members at h = 0.217]
        |        |--leaf "13" 
        |        `--[dendrogram w/ 2 branches and 2 members at h = 0.117]
        |           |--leaf "10" 
        |           `--leaf "16" 
        `--[dendrogram w/ 2 branches and 7 members at h = 1.7]
           |--[dendrogram w/ 2 branches and 5 members at h = 0.539]
           |  |--leaf "7" 
           |  `--[dendrogram w/ 2 branches and 4 members at h = 0.223]
           |     |--leaf "8" 
           |     `--[dendrogram w/ 2 branches and 3 members at h = 0.183]
           |        |--leaf "4" 
           |        `--[dendrogram w/ 2 branches and 2 members at h = 0.107]
           |           |--leaf "2" 
           |           `--leaf "3" 
           `--[dendrogram w/ 2 branches and 2 members at h = 0.698]
              |--leaf "1" 
              `--leaf "5" 


       
---------------------------------
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[Jtreeview-users] Is java treeview compatible with Win VISTA?

[fangm55555 <fan...@gm...>]

Hi, I tried many times, it seems that the latest release of java treeview can't work at all in VISTA. Could you give me some suggestion? Thank you!
Ming

2008-04-25 



fangm55555 

Re: [Jtreeview-users] node flipping

[Alok S. <alo...@gm...>]

Flipping of gene nodes has not yet been implemented. JTV is not very  
actively developed right now, but since you are the second person to  
request this,

http://sourceforge.net/tracker/index.php? 
func=detail&aid=1753534&group_id=84593&atid=573301

  I will try and find time over the next week or next weekend to  
implement it.

-Alok


On Apr 3, 2008, at 1:38 PM, Jan Krzysztof Blusztajn wrote:

> Hi,
>
> I am trying to flip nodes of genes.  I select a gene node and use the
> "Flip tree node" option under Analysis but this flips the arrays.  Is
> it possible to flip the gene nodes?
>
> Many thanks,
>
> Jan
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
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> _______________________________________________
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> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] node flipping

[Jan K. B. <jbl...@bu...>]

Hi,

I am trying to flip nodes of genes.  I select a gene node and use the  
"Flip tree node" option under Analysis but this flips the arrays.  Is  
it possible to flip the gene nodes?

Many thanks,

Jan

Re: [Jtreeview-users] Help with jtreeview

[Alok S. <alo...@gm...>]

Dear Annie,

You can adjust the scale using the pixel setttings. Load the ratio =20
data, then go to settings->pixel settings, and then in the contrast =20
section you can enter a contrast value in the box labelled "value" or =20=

adjust the slider. Also, you can log transform within treeview now =20
within the settings menu but (embarssingly) I haven' updated JTV on =20
this laptop so I can't tell you exactly what I named the controls, =20
but they're on the same settings panel.  There is some slightly out =20
of date documentation here:

http://jtreeview.sourceforge.net/docs/JTVUserManual/=20
ch02s04.html#ch2_settings_dcolor

Hope this helps.

Alok


On Oct 28, 2007, at 6:32 PM, Annie Chiu Eng Wong wrote:

> Hi there,
>
> Thank you for the jtreeview software. I am a researcher from the =20
> University of Melbourne and I hope you don=92t mind my abrupt email =20=

> asking for some advice.
>
>
>
> I have some microarray time point data (log2 transformed signal =20
> intensity level for each gene) that I have clustered using K-mean =20
> clustering implemented in Cluster. I would like to display the =20
> results as a heat map in jtreeview. I realised that the difference =20
> between each time point for each gene is better displayed when =20
> ratio is used instead of the log2 transformed signal intensity =20
> level. I understand this is because the pixel setting is such that =20
> =93red=94 is for positive and =93green=94 is for negative while black =
is =20
> for =93zero=94. The scale is not sensitive enough to capture all the =20=

> positive value of the signal intensity level.
>
>
>
> I wonder whether there is a way that I can change the setting such =20
> that it allows me to display the normalized signal intensity data =20
> in red and green with red denoting high expression while green low =20
> expression.
>
>
>
> Your kind attention is very much appreciated and I look forward to =20
> your reply.
>
>
>
> Regards, Annie
>
>
>
> Annie CE WONG (PhD),
> Research Fellow,
> Plant Molecular Biology and Biotechnology Laboratory,
> ARC Centre of Excellence for Integrative Legume Research,
> School of Agriculture and Food Systems,
> University of Melbourne,
> Parkville,
> Victoria 3010,
> Australia.
>
> Tel : 03 8344 5013/6326
>
>
>
> ----------------------------------------------------------------------=20=

> ---
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a =20
> browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/=20
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] Help with jtreeview

[Annie C. E. W. <ac...@un...>]

Hi there,

Thank you for the jtreeview software. I am a researcher from the
University of Melbourne and I hope you don't mind my abrupt email asking
for some advice.

=20

I have some microarray time point data (log2 transformed signal
intensity level for each gene) that I have clustered using K-mean
clustering implemented in Cluster. I would like to display the results
as a heat map in jtreeview. I realised that the difference between each
time point for each gene is better displayed when ratio is used instead
of the log2 transformed signal intensity level. I understand this is
because the pixel setting is such that "red" is for positive and "green"
is for negative while black is for "zero". The scale is not sensitive
enough to capture all the positive value of the signal intensity level.=20

=20

I wonder whether there is a way that I can change the setting such that
it allows me to display the normalized signal intensity data in red and
green with red denoting high expression while green low expression.

=20

Your kind attention is very much appreciated and I look forward to your
reply.

=20

Regards, Annie

=20

Annie CE WONG (PhD),
Research Fellow,
Plant Molecular Biology and Biotechnology Laboratory,
ARC Centre of Excellence for Integrative Legume Research,
School of Agriculture and Food Systems,
University of Melbourne,
Parkville,
Victoria 3010,
Australia.

Tel : 03 8344 5013/6326

=20

[Jtreeview-users] Clustersoftware fpr generating consistent alternatives of strategies

[Thorsten O. <tho...@ly...>]

Hello,

i just wanted to know if there is some chance that you could help us with=20
our problem running a clustering process like considered. Some weeks ago i=
=20
sent some archives for explaining more adequately what we're up to do and=20
what's the expectes result.

It would be very kind hearing from whether there is support possible or=20
not.

Thanks a lot in advance, regards!

Thorsten


Thorsten Ortjohann
Consultant Business Process Management
Lynx-Consulting AG
Johanniskirchplatz 6
D-33615 Bielefeld
Fon: +49 521 5247-0
Fax: +49 521 5247-250
Mobil: +49 175 22 85 490


Company and Management Headquarters:
Lynx-Consulting AG, Johanniskirchplatz 6, D-33615 Bielefeld
Fon: +49 521 5247-0, Fax: +49 521 5247-250, www.lynx.de

Court Registration: Amtsgericht Bielefeld HRB 35946
Members of the Management Board authorised to represent: Peter H=C3=BCsener
Chairman of the Supervisory Board: Hans-Joachim Rosowski

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