Hi all,

I am a novice user of the heatmap.2 function in the Bioconductor gplots package.

I am trying to create a heatmap diagram from a hierarchical clustering result based on the complete linkage and the pearson correlations as the distance metrics.

After reading the help page for heatmap.2, it seems that it calls the distfun and hclustfun with the default settings.  Is that the same as doing the below?
> hr<-hclust(as.dist(1-cor(t(data), method="pearson")), method="complete)
> hc<-hclust(as.dist(1-cor(data, method="pearson")), method="complete)
> heatmap.2(data, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), scale="row")

When I just do the following, I get a completely different heatmap:
> heatmap.2(data, scale="row")

Could you please tell me how calling the heatmap.2 without specifying the Rowv and Colv results in different heatmaps?  The help page says that when Rowv and Colv are null, it calls hclust and dist with default parameters, which is what I had done in the first case.

Thank you so much for your help.

regards,
Elizabeth




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