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Old 07-09-2014, 08:28 AM   #3
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Join Date: Sep 2012
Posts: 130

Originally Posted by WhatsOEver View Post
You could start trying a different method for the hierarchical clustering (I think the standard is average, but I'm not really sure on this ->
In my case, ward's method performed much better for clustering of gene expressions.
Thanks for that suggestion. Switching the hclust method to ward had very noticeable results.

I guess my problem is really with the range of values. Most of the values end up in a small subset of the color range. My initial hope was the scale parameter would solve that, but it only shifts the distribution. The colors at the ends of the range are essentially not represented. Regardless of how good the clustering is, it's difficult to actually see the results. Here is an example of what I mean (the color key and histogram is the important part):
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