[BioC] hclust - order of rows/columns

[Lina Hultin-Rosenberg]

Dear all,

I am using heatmap.2 to create a hierarchical clustering heatmap of some
gene expression data. I am wondering how the order of the rows and columns
affects the resulting dendogram/heatmap. I have seen that different order of
rows gives different heatmaps. Is it valid to order the rows or columns in
an order that seem logic to the study before I do the hierarchical
clustering or should I rather randomize the order? As I understand, the
hierarchical clustering will break the original order if it "violates" the
clusters.  

Thank you!

Best regards,
Lina Hultin Rosenberg

________________________________
Lina Hultin Rosenberg
Msc Molecular Biotechnology
Evolutionary Biology Department
Uppsala University
Norbyvägen 18
752 36 Uppsala
Phone: +46-18-4716444
Email: lina.hultin.rosenberg at ebc.uu.se