I have a fundamental question in microarray data analysis. The defaults of almost every heat map function in R does the hierarchical clustering first, then scales the rows then displays the image. But as you can imagine, doing the scaling first and clustering second significantly changes the appearance of a heat map as well as the clustering.
So my main question is, in their essence, is both solutions acceptable? Or only one of the strategies is correct? If so, why not the other one?
Thanks a lot!