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=

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