Re: [Jtreeview-users] Help with jtreeview
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From: Alok S. <alo...@gm...> - 2007-10-29 11:36:43
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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 |