Re: [Jtreeview-users] question for selection of different genes using the dendogram

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

The behavior is expected. However, if you open the CDT file in excel  
you can add a common annotation to all the genes that you wish to see  
placed together.  You don't need to enter a complete gene name, you  
can enter a substring of any annotation. It would probably be better  
if there were an "add to selection" option or something, instead of  
it always replacing the current selection.

Incidentally, you can append to current selection in the scatterplot  
view if you hold down the control key. But that doesn't work anywhere  
else. You can scatterplot index against index to get the idea- index  
is just the distance of the gene from the top of the dendrogram. To  
use the scatterplot, you may need to select "linked" from the style  
menu when you open a new, and then select "Analysis->scatterplot".

	-Alok

On Mar 16, 2007, at 12:01 PM, jeremie poschmann wrote:

> Hi Alok
> thanks for taking the time to answer me. You answered exactly my  
> questions,
> However I cant accumulate genes in the find genes dialog. Each time
> the previously searched gene is gone, only the currently selected gene
> is shown. Is this normal or do I have a problem with the program ?
> thank you
> cheers
> jeremie
>
> 2007/3/16, Alok Saldanha <alo...@gm...>:
>> I'm not entirely sure what you're asking.
>> If you can give the genes similar annotations, you can view them in a
>> separate window using the following:
>>
>> 1) Open Analysis->Find Genes... dialog
>> 2) Type in the relevant annotation
>> 3) Press return to initiate search
>> 4) Click "All" to select all
>> 5) Click "Summary Popup"
>>
>> At any time, you can click "Analysis->Summary popup" to get  a
>> summary popup of the currently selected genes. There's currently no
>> way to select discontinuous ranges manually, however- the only way in
>> dendrogram view is by searching for annotation. The other way
>> currently to select discontinuous ranges is selecting points in a
>> scatterplot. This is entirely a UI issue.
>>
>> Hope this helps,
>> Alok
>>
>> On Mar 15, 2007, at 3:54 PM, jeremie poschmann wrote:
>>
>> > HI,
>> > I have a dendrogram with several hundred genes which are ordered by
>> > hirarchical clustering.  I would like to know if its possible to
>> > choose some different genes which arent related and then put them
>> > below each other in the dendrogram, so that I can compare them  
>> to the
>> > total set of genes
>> > Please help me
>> > thank you very much
>> > all the best
>> >
>> > --
>> > Jeremie Poschmann
>> > PhD student
>> > Centre de Recherche Guy Bernier
>> > Hopital Rosemont-Maissonneuve
>> > 5415 Boul. de l'Assomption
>> > Montreal Quebec
>> > H1T 2M4
>> > Tel 514 252 3400 ext. 3349
>> >
>> >  
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>
>
> -- 
> Jeremie Poschmann
> PhD student
> Centre de Recherche Guy Bernier
> Hopital Rosemont-Maissonneuve
> 5415 Boul. de l'Assomption
> Montreal Quebec
> H1T 2M4
> Tel 514 252 3400 ext. 3349