[R] Questions concerning HOPACH

W. Katy linlicc at hotmail.com
Mon Jul 23 19:02:05 CEST 2007


I have been tried to apply hopach HOPACH in R to cluster some genes.  My 
data is a binary matrix.  It works well for the whole set of genes (say, 
1000 genes).  Then I selected a subset of the genes (say 300 genes).  These 
genes are selected based on the regression analysis results for each of the 
1000 genes and only those with highly correlations with specific sample 
types got selected.  With the subset of the genes (300), when I run HOPACH, 
the hopach stuck there for ever, and the CPU occupation kePT 100% as well.  

So I am wondering if there is any restrictions in applying HOPACH commend. 
Apparently, this stuck is not because of memory issue based on the CPU 
monitor.  I will really appreicate any share of comments, thoughts or 

Thanks very much!

Regards, Katy

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