question regarding clustergram

[James Anderson]

Hi,

I am using the clustergram for the heatmap and hierarchical clustering for the microarray data I am working on. One feature I want to have is to have a group membership of control and treated designated as different colors shown in a horizontal bar right above the heatmap and below the dendrogram. I was looking into the arguments and found that the ColumnGroupMarker is the one which is closet to what I want, but still not exactly what I need, because the group membership of ColumnGroupMarker is based on the how different samples are clustered together dendrogram. I want something that is purely based on the phenotype label of the samples, regardless of how samples are clustered based on different phenotypes or not. Does anybody have any clue on how to do this?

Thanks a bunch,

James

[ImageAnalyst]

James Anderson
I have a feeling this is closely related to some toolbox. What
toolboxes are you using (type "ver")? Also a picture to show what you
got and what you wanted could be helpful.

[James Anderson]

Hi ImageAnalyst,

Thanks for your email. Please see below for the version of toolboxes.

MATLAB Version 7.12 (R2011a)
Bioinformatics Toolbox Version 3.8 (R2011a+)
Statistics Toolbox Version 7.5 (R2011a)

Sorry that I don't even know how to paste picture here. But if you type "doc clustergram" in matlab, the last picture (heamap and dendrogram of a matrix with 614 rows (genes) and 7 columns (samples)), you see that the first 5 samples have one color in the bar between the heatmap and dendrogram, the other 7 samples have the same color, because the samples were clustered that way. What I want is really simple: If I assume among the 7 samples, sample 1,3,5 are control and samples 2,4,6,7 are treated, I want to create a similar horizontal bar between the heatmap and the dendrogram where samples 1,3,5 have one color and samples 2,4,6,7 have another color, regardless of how different samples are clustered together.

Thanks,

-James




ImageAnalyst <imagea...@mailinator.com> wrote in message <98505310-bae2-45d1...@hd1g2000vbb.googlegroups.com>...

[ImageAnalyst]

I don't have those toolboxes. Hopefully someone else will help. You
might try
http://www.mathworks.com/matlabcentral/answers/

and
http://www.mathworks.com/matlabcentral/answers/?term=tag%3Atutorial,
particularly:
http://www.mathworks.com/matlabcentral/answers/7924-where-can-i-upload-images-and-files-for-use-on-matlab-answers