[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.

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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

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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.

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

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Regards, Annie

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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

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